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Chlorine in PDB 9f47: Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii

Protein crystallography data

The structure of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii, PDB code: 9f47 was solved by J.Duan, A.Rutz, E.Hofmann, T.Happe, G.Kurisu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.26 / 2.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 169, 169, 127, 90, 90, 90
R / Rfree (%) 24.2 / 29.8

Other elements in 9f47:

The structure of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Iron (Fe) 28 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii (pdb code 9f47). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii, PDB code: 9f47:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 9f47

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Chlorine binding site 1 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl706

b:73.5
occ:1.00
 OE2 A:GLU477 2.7 74.4 1.0
OE1 A:GLU470 3.2 82.6 1.0
HB3 A:GLU470 3.4 76.9 1.0
O A:ILE471 3.6 76.9 1.0
CD A:GLU477 3.7 75.4 1.0
OE1 A:GLU477 4.1 71.1 1.0
CD A:GLU470 4.3 79.1 1.0
CB A:GLU470 4.3 64.1 1.0
H A:ILE471 4.4 81.2 1.0
HG3 A:GLU470 4.6 87.5 1.0
HA A:THR473 4.6 84.8 1.0
CG A:GLU470 4.6 72.9 1.0
C A:ILE471 4.7 70.3 1.0
HG23 A:THR473 4.7 96.4 1.0
HB A:ILE471 4.7 95.8 1.0
N A:ILE471 4.7 67.7 1.0
OG1 A:THR473 4.8 71.3 1.0
HB2 A:GLU470 4.8 76.9 1.0

Chlorine binding site 2 out of 10 in 9f47

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Chlorine binding site 2 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl707

b:101.2
occ:1.00
 O A:GLY323 2.8 87.9 1.0
OD1 A:ASP325 3.4 98.1 1.0
OD2 A:ASP325 3.5 86.4 1.0
O A:LYS285 3.7 83.3 1.0
CG A:ASP325 3.8 90.5 1.0
O A:LEU280 3.8 93.2 1.0
C A:GLY323 3.9 78.9 1.0
HG23 A:VAL287 4.0 94.1 1.0
HA3 A:GLY323 4.1 96.5 1.0
HA A:LEU280 4.1 101.1 1.0
HA2 A:GLY323 4.4 96.5 1.0
CA A:GLY323 4.4 80.4 1.0
HG21 A:VAL287 4.7 94.1 1.0
HD23 A:LEU280 4.7 92.4 1.0
H A:LYS285 4.7 87.2 1.0
HD22 A:LEU280 4.7 92.4 1.0
CG2 A:VAL287 4.7 78.4 1.0
C A:LEU280 4.8 87.7 1.0
HB A:VAL287 4.8 87.4 1.0
H A:VAL287 4.8 85.6 1.0
CA A:LEU280 4.9 84.2 1.0
C A:LYS285 4.9 83.3 1.0
O A:THR282 4.9 73.5 1.0
HA A:VAL324 4.9 72.6 1.0

Chlorine binding site 3 out of 10 in 9f47

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Chlorine binding site 3 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl708

b:91.3
occ:1.00
 HD21 A:ASN183 3.2 112.9 1.0
HG11 A:VAL174 3.3 137.1 1.0
HE1 A:MET147 3.6 93.0 1.0
ND2 A:ASN183 3.6 94.1 1.0
HE2 A:TYR121 3.8 115.1 1.0
HD22 A:ASN183 3.9 112.9 1.0
HB A:ILE184 4.0 134.3 1.0
H A:ILE184 4.0 123.9 1.0
HH A:TYR121 4.1 126.3 1.0
HD23 A:LEU125 4.2 107.4 1.0
HG21 A:VAL174 4.3 104.9 1.0
CG1 A:VAL174 4.3 114.2 1.0
CG A:ASN183 4.4 94.6 1.0
HG12 A:ILE144 4.4 106.9 1.0
HD11 A:ILE144 4.4 101.6 1.0
CE A:MET147 4.5 77.5 1.0
HD13 A:ILE144 4.5 101.6 1.0
HD21 A:LEU125 4.6 107.4 1.0
OD1 A:ASN183 4.6 87.2 1.0
H A:MET185 4.6 103.7 1.0
HG12 A:VAL174 4.6 137.1 1.0
CE2 A:TYR121 4.7 95.9 1.0
HE3 A:MET147 4.7 93.0 1.0
HD11 A:ILE122 4.7 99.1 1.0
CD2 A:LEU125 4.7 89.5 1.0
HG13 A:VAL174 4.8 137.1 1.0
N A:ILE184 4.8 103.2 1.0
CD1 A:ILE144 4.8 84.7 1.0
HD13 A:ILE122 4.9 99.1 1.0
OH A:TYR121 4.9 105.3 1.0
HB2 A:MET185 4.9 105.0 1.0
CB A:ILE184 4.9 112.0 1.0
HD22 A:LEU125 4.9 107.4 1.0
HB A:VAL174 5.0 121.6 1.0

Chlorine binding site 4 out of 10 in 9f47

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Chlorine binding site 4 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl709

b:94.0
occ:1.00
 HG11 A:VAL474 2.7 103.7 1.0
CG1 A:VAL474 3.4 86.4 1.0
HD1 A:TRP404 3.5 80.8 1.0
HG13 A:VAL474 3.5 103.7 1.0
HG12 A:VAL474 3.6 103.7 1.0
HG22 A:ILE403 3.6 73.0 1.0
HA A:TRP404 3.7 64.5 1.0
HG3 A:GLU407 3.8 98.9 1.0
OH A:TYR620 4.2 77.2 1.0
HE2 A:TYR620 4.2 74.7 1.0
HB2 A:TRP404 4.3 80.7 1.0
CD1 A:TRP404 4.4 67.3 1.0
CG2 A:ILE403 4.4 60.9 1.0
HG21 A:ILE403 4.5 73.0 1.0
HD11 A:ILE616 4.5 94.3 1.0
CA A:TRP404 4.6 53.7 1.0
HG21 A:VAL474 4.7 94.0 1.0
HH A:TYR620 4.7 92.6 1.0
HG23 A:ILE403 4.7 73.0 1.0
CB A:VAL474 4.8 65.5 1.0
CB A:TRP404 4.8 67.2 1.0
CG A:GLU407 4.8 82.4 1.0
HD13 A:ILE616 4.8 94.3 1.0
CE2 A:TYR620 4.9 62.2 1.0
HB A:VAL474 4.9 78.5 1.0
HZ2 A:LYS619 5.0 91.8 1.0
HB2 A:GLU407 5.0 78.1 1.0
N A:TRP404 5.0 55.9 1.0
CZ A:TYR620 5.0 70.0 1.0

Chlorine binding site 5 out of 10 in 9f47

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Chlorine binding site 5 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl710

b:94.8
occ:1.00
 HA A:LYS579 3.2 73.1 1.0
HH21 A:ARG450 3.6 95.1 1.0
HG23 A:THR580 3.6 98.3 1.0
O A:PRO578 3.7 73.2 1.0
H A:THR580 3.8 82.8 1.0
HB2 A:GLN577 3.9 82.3 1.0
O A:GLY574 4.1 79.4 1.0
HZ3 A:LYS584 4.1 146.2 1.0
O A:GLN577 4.1 56.8 1.0
HH12 A:ARG591 4.1 78.4 1.0
CA A:LYS579 4.1 60.9 1.0
HE2 A:LYS584 4.2 143.7 1.0
HG3 A:LYS579 4.2 99.2 1.0
HA2 A:GLY575 4.3 89.6 1.0
NH2 A:ARG450 4.4 79.2 1.0
C A:PRO578 4.4 69.9 1.0
N A:THR580 4.4 69.0 1.0
HH22 A:ARG450 4.4 95.1 1.0
N A:LYS579 4.5 70.7 1.0
CG2 A:THR580 4.6 81.9 1.0
HH22 A:ARG591 4.7 66.0 1.0
C A:GLN577 4.7 64.9 1.0
NZ A:LYS584 4.7 121.8 1.0
HZ1 A:LYS584 4.7 146.2 1.0
C A:LYS579 4.7 73.1 1.0
HD21 A:LEU588 4.8 96.0 1.0
CB A:GLN577 4.8 68.6 1.0
HG2 A:LYS579 4.9 99.2 1.0
CE A:LYS584 4.9 119.7 1.0
CG A:LYS579 4.9 82.6 1.0
H A:GLN577 4.9 70.0 1.0
NH1 A:ARG591 4.9 65.3 1.0
HD3 A:LYS584 4.9 124.2 1.0
HG22 A:THR580 5.0 98.3 1.0

Chlorine binding site 6 out of 10 in 9f47

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Chlorine binding site 6 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl711

b:100.5
occ:1.00
 HB1 A:ALA269 2.9 81.4 1.0
HB2 A:LEU216 3.3 98.5 1.0
HD2 A:HIS254 3.3 121.6 1.0
HH A:TYR249 3.5 125.8 1.0
H A:LEU216 3.5 96.3 1.0
CB A:ALA269 3.7 67.8 1.0
HA A:ALA269 3.9 111.9 1.0
N A:LEU216 3.9 80.3 1.0
CD2 A:HIS254 3.9 101.3 1.0
HB2 A:ALA269 3.9 81.4 1.0
OH A:TYR249 4.0 104.8 1.0
NE2 A:HIS254 4.0 106.2 1.0
HA A:LYS215 4.0 96.2 1.0
HB2 A:TYR428 4.1 90.9 1.0
O A:ALA269 4.1 95.4 1.0
CB A:LEU216 4.2 82.1 1.0
HA A:LEU216 4.3 87.1 1.0
CA A:ALA269 4.3 93.3 1.0
HG13 A:VAL214 4.4 101.8 1.0
CA A:LEU216 4.4 72.6 1.0
HB3 A:ALA269 4.5 81.4 1.0
C A:LYS215 4.5 78.8 1.0
HB2 A:LYS427 4.5 97.6 1.0
HB3 A:LEU216 4.6 98.5 1.0
O A:VAL214 4.6 88.6 1.0
HB A:ILE424 4.6 98.5 1.0
HD13 A:LEU216 4.6 79.8 1.0
C A:ALA269 4.6 87.5 1.0
HA A:TYR428 4.7 93.3 1.0
CA A:LYS215 4.7 80.2 1.0
HG22 A:VAL214 4.8 88.3 1.0
HB3 A:LYS427 4.8 97.6 1.0
CB A:TYR428 4.9 75.7 1.0
H A:TYR428 4.9 76.2 1.0
HD12 A:ILE424 4.9 91.4 1.0
HB3 A:TYR428 5.0 90.9 1.0
HG13 A:ILE424 5.0 111.8 1.0
HD3 A:LYS427 5.0 87.8 1.0

Chlorine binding site 7 out of 10 in 9f47

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Chlorine binding site 7 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl706

b:103.1
occ:1.00
 HZ2 B:LYS628 2.7 127.1 1.0
OD1 B:ASP622 2.8 99.1 1.0
OD2 B:ASP622 2.9 90.6 1.0
CG B:ASP622 3.2 98.1 1.0
NZ B:LYS628 3.3 105.9 1.0
HZ3 B:LYS628 3.3 127.1 1.0
HZ1 B:LYS628 3.5 127.1 1.0
O B:TYR620 3.7 86.0 1.0
O B:LYS619 3.8 87.7 1.0
HA B:TYR620 4.0 98.8 1.0
C B:TYR620 4.3 72.8 1.0
C B:LYS619 4.4 71.1 1.0
CA B:TYR620 4.5 82.4 1.0
HD2 B:LYS628 4.6 93.3 1.0
CE B:LYS628 4.6 99.2 1.0
CB B:ASP622 4.7 89.3 1.0
N B:TYR620 4.7 67.5 1.0
HD3 B:LYS628 4.9 93.3 1.0
HE3 B:LYS628 5.0 119.0 1.0
CD B:LYS628 5.0 77.8 1.0

Chlorine binding site 8 out of 10 in 9f47

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Chlorine binding site 8 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl707

b:73.7
occ:1.00
 OE2 B:GLU477 2.6 72.0 1.0
OE1 B:GLU470 3.3 89.5 1.0
CD B:GLU477 3.4 76.2 1.0
OE1 B:GLU477 3.5 79.7 1.0
HB3 B:GLU470 4.0 61.3 1.0
O B:ILE471 4.1 80.1 1.0
OG1 B:THR473 4.3 62.5 1.0
CD B:GLU470 4.5 83.9 1.0
HG1 B:THR473 4.6 75.0 1.0
HA B:THR473 4.6 73.3 1.0
HG23 B:THR473 4.7 94.9 1.0
H B:ILE471 4.8 77.0 1.0
CB B:GLU470 4.9 51.1 1.0
CG B:GLU477 4.9 69.2 1.0
HG3 B:GLU470 5.0 83.4 1.0

Chlorine binding site 9 out of 10 in 9f47

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Chlorine binding site 9 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl708

b:86.5
occ:1.00
 O B:GLY323 3.0 75.9 1.0
OD1 B:ASP325 3.5 93.0 1.0
O B:LEU280 3.6 77.2 1.0
OD2 B:ASP325 3.7 80.4 1.0
O B:LYS285 3.8 76.4 1.0
HA B:LEU280 4.0 97.5 1.0
CG B:ASP325 4.0 90.0 1.0
C B:GLY323 4.0 79.0 1.0
HG23 B:VAL287 4.1 85.5 1.0
HA3 B:GLY323 4.1 100.9 1.0
HD23 B:LEU280 4.4 92.3 1.0
CA B:GLY323 4.5 84.1 1.0
C B:LEU280 4.5 78.1 1.0
HA2 B:GLY323 4.6 100.9 1.0
CA B:LEU280 4.7 81.2 1.0
O B:THR282 4.7 81.5 1.0
H B:LYS285 4.7 72.5 1.0
HB B:VAL287 4.8 84.1 1.0
HG21 B:VAL287 4.8 85.5 1.0
H B:VAL287 4.9 83.2 1.0
CG2 B:VAL287 4.9 71.2 1.0
HA B:VAL324 4.9 75.9 1.0
HB3 B:LEU280 5.0 93.0 1.0
C B:LYS285 5.0 72.1 1.0

Chlorine binding site 10 out of 10 in 9f47

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Chlorine binding site 10 out of 10 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl709

b:84.2
occ:1.00
 HB2 B:GLN577 3.4 83.9 1.0
HH12 B:ARG591 3.4 71.4 1.0
HG23 B:THR580 3.4 82.9 1.0
O B:GLY574 3.6 71.3 1.0
O B:PRO578 3.7 80.7 1.0
HA B:LYS579 3.7 90.9 1.0
HH21 B:ARG450 4.1 103.2 1.0
HA2 B:GLY573 4.1 87.3 1.0
H B:THR580 4.1 92.0 1.0
HD21 B:LEU588 4.2 85.8 1.0
O B:GLN577 4.2 68.5 1.0
HE2 B:LYS584 4.2 142.9 1.0
NH1 B:ARG591 4.2 59.5 1.0
O B:GLY573 4.3 69.5 1.0
CB B:GLN577 4.3 69.9 1.0
CG2 B:THR580 4.3 69.0 1.0
HB3 B:GLN577 4.5 83.9 1.0
C B:PRO578 4.5 76.7 1.0
HA2 B:GLY575 4.5 90.9 1.0
C B:GLY573 4.5 66.9 1.0
HH22 B:ARG450 4.5 103.2 1.0
HH22 B:ARG591 4.5 80.5 1.0
HG22 B:THR580 4.6 82.9 1.0
CA B:LYS579 4.6 75.8 1.0
HG3 B:LYS579 4.6 114.7 1.0
C B:GLN577 4.6 71.6 1.0
HH11 B:ARG591 4.6 71.4 1.0
NH2 B:ARG450 4.6 86.0 1.0
C B:GLY574 4.6 72.4 1.0
N B:THR580 4.6 76.6 1.0
HG21 B:THR580 4.7 82.9 1.0
H B:GLN577 4.7 84.5 1.0
CA B:GLY573 4.8 72.8 1.0
N B:LYS579 4.9 78.8 1.0
CA B:GLN577 4.9 77.5 1.0

Reference:

J.Duan, A.Rutz, A.Kawamoto, S.Naskar, K.Edenharter, S.Leimkuehler, E.Hofmann, T.Happe, G.Kurisu. A Zinc Binding Four-Helix Domain Stabilizes the Dimeric Structure of O2-Stable [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii To Be Published.
Page generated: Sat Feb 8 17:32:07 2025

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