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Chlorine in PDB 6pbz: Crystal Structure of Escherichia Coli Gppa

Enzymatic activity of Crystal Structure of Escherichia Coli Gppa

All present enzymatic activity of Crystal Structure of Escherichia Coli Gppa:
3.6.1.40;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Gppa, PDB code: 6pbz was solved by H.Song, G.X.Shaw, C.Wang, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.46 / 2.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.829, 162.510, 165.669, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Escherichia Coli Gppa (pdb code 6pbz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Escherichia Coli Gppa, PDB code: 6pbz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6pbz

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Chlorine binding site 1 out of 8 in the Crystal Structure of Escherichia Coli Gppa


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 Escherichia Coli Gppa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:95.5
occ:1.00
 O A:TRP205 3.7 73.3 1.0
N A:TRP205 3.9 77.7 1.0
CA A:GLY204 4.2 76.9 1.0
CD2 A:TRP205 4.2 69.6 1.0
CE2 A:TRP205 4.3 68.8 1.0
CE3 A:TRP205 4.4 69.9 1.0
O A:HOH701 4.4 82.4 1.0
CZ2 A:TRP205 4.5 69.1 1.0
C A:GLY204 4.5 77.0 1.0
O A:HOH677 4.6 80.8 1.0
CZ3 A:TRP205 4.6 69.4 1.0
CH2 A:TRP205 4.6 69.0 1.0
C A:TRP205 4.6 75.1 1.0
CG A:TRP205 4.7 70.9 1.0
NE1 A:TRP205 4.7 68.0 1.0
CA A:TRP205 4.8 75.7 1.0
CD1 A:TRP205 4.9 68.7 1.0

Chlorine binding site 2 out of 8 in 6pbz

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Chlorine binding site 2 out of 8 in the Crystal Structure of Escherichia Coli Gppa


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 Escherichia Coli Gppa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:81.8
occ:1.00
 NE1 A:TRP205 3.0 68.0 1.0
N A:GLN282 3.4 69.0 1.0
CD1 A:TRP205 3.7 68.7 1.0
O A:HOH635 3.8 76.3 1.0
CA A:ILE281 4.0 63.1 1.0
CG A:GLN282 4.1 79.2 1.0
CB A:GLN282 4.1 75.7 1.0
CE2 A:TRP205 4.1 68.8 1.0
C A:ILE281 4.2 64.8 1.0
CA A:GLN282 4.3 73.6 1.0
N A:CYS283 4.3 75.9 1.0
CG2 A:ILE281 4.3 59.8 1.0
O A:CYS283 4.4 63.9 1.0
O A:ASN280 4.5 69.4 1.0
CB A:CYS208 4.5 62.4 1.0
CB A:ILE281 4.6 59.8 1.0
CZ2 A:TRP205 4.7 69.1 1.0
CG1 A:ILE281 4.7 58.2 1.0
C A:GLN282 4.8 75.5 1.0
N A:CYS208 4.9 66.7 1.0

Chlorine binding site 3 out of 8 in 6pbz

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Chlorine binding site 3 out of 8 in the Crystal Structure of Escherichia Coli Gppa


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 Escherichia Coli Gppa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:81.9
occ:1.00
 O A:HOH709 2.9 54.1 1.0
N A:ASP228 3.1 61.6 1.0
NZ A:LYS235 3.3 62.8 1.0
CG A:ASP228 3.5 69.7 1.0
OD1 A:ASP228 3.5 69.7 1.0
CE A:LYS235 3.5 64.3 1.0
CB A:MET227 3.5 60.9 1.0
OD2 A:ASP228 3.6 73.3 1.0
CA A:MET227 3.7 61.5 1.0
C A:MET227 3.9 60.7 1.0
CB A:ASP228 4.1 68.2 1.0
CA A:ASP228 4.1 64.5 1.0
CD1 C:TYR486 4.2 57.7 1.0
CE1 C:TYR486 4.2 56.0 1.0
O C:HOH642 4.3 72.0 1.0
CG A:MET227 4.4 62.7 1.0
O A:ASP228 4.5 59.1 1.0
CD A:LYS235 4.6 63.6 1.0
C A:ASP228 4.7 63.4 1.0

Chlorine binding site 4 out of 8 in 6pbz

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Chlorine binding site 4 out of 8 in the Crystal Structure of Escherichia Coli Gppa


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 Escherichia Coli Gppa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:0.2
occ:1.00
 CG2 B:THR154 3.1 98.8 1.0
CD B:ARG118 3.6 97.2 1.0
NE2 B:GLN122 3.8 90.1 1.0
CG B:ARG118 3.9 95.0 1.0
NE B:ARG118 4.0 98.3 1.0
NE2 B:GLN153 4.2 0.4 1.0
N B:THR154 4.2 99.6 1.0
O B:ALA152 4.2 95.0 1.0
CB B:THR154 4.6 99.0 1.0
CA B:GLN153 4.7 0.1 1.0
CD B:GLN153 4.8 0.9 1.0
CD B:GLN122 4.8 89.7 1.0
OE1 B:GLN153 5.0 0.3 1.0
C B:GLN153 5.0 99.9 1.0

Chlorine binding site 5 out of 8 in 6pbz

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Chlorine binding site 5 out of 8 in the Crystal Structure of Escherichia Coli Gppa


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 Escherichia Coli Gppa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:92.9
occ:1.00
 NE2 C:GLN416 2.7 51.9 1.0
ND1 C:HIS414 2.9 53.9 1.0
O C:GLN416 3.3 64.4 1.0
CA C:HIS414 3.5 52.2 1.0
CD C:GLN416 3.6 52.7 1.0
CA C:PRO421 3.7 50.0 1.0
CG C:GLN416 3.8 52.9 1.0
CG C:HIS414 3.8 54.3 1.0
CB C:HIS414 3.8 52.5 1.0
CB C:PRO421 3.8 49.7 1.0
CG C:PRO421 3.9 49.4 1.0
O C:HIS414 3.9 55.1 1.0
CE1 C:HIS414 3.9 53.2 1.0
C C:HIS414 3.9 55.1 1.0
C C:GLN416 4.2 62.5 1.0
N C:PRO421 4.3 53.4 1.0
O C:LEU413 4.3 50.6 1.0
CB C:ALA424 4.4 46.7 1.0
N C:GLN416 4.4 63.2 1.0
O C:VAL419 4.5 55.7 1.0
CD1 A:LEU410 4.6 56.8 1.0
CD C:PRO421 4.6 52.0 1.0
N C:HIS414 4.6 51.9 1.0
CA C:GLN416 4.7 60.6 1.0
OE1 C:GLN416 4.8 50.9 1.0
C C:PRO421 4.8 49.7 1.0
CB C:GLN416 4.9 56.3 1.0
O C:HOH621 4.9 68.2 1.0
C C:LEU413 4.9 51.4 1.0
C C:PRO420 4.9 57.6 1.0
N C:GLN415 4.9 58.4 1.0
O C:PRO421 4.9 47.2 1.0
CD2 C:HIS414 5.0 54.4 1.0

Chlorine binding site 6 out of 8 in 6pbz

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Chlorine binding site 6 out of 8 in the Crystal Structure of Escherichia Coli Gppa


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 Escherichia Coli Gppa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:90.4
occ:1.00
 O C:HOH620 3.2 67.4 1.0
CA C:GLN372 3.7 59.1 1.0
N C:GLN375 3.7 54.2 1.0
CD C:PRO374 3.8 50.0 1.0
CG C:GLN372 3.8 68.4 1.0
O C:GLN372 3.9 55.2 1.0
C C:GLN372 3.9 56.8 1.0
CB C:GLN372 3.9 63.7 1.0
CB C:GLN375 4.1 61.0 1.0
CG C:PRO374 4.1 50.0 1.0
CG C:GLN375 4.1 67.9 1.0
CB C:PRO374 4.1 51.0 1.0
N C:PRO374 4.3 51.4 1.0
OE1 C:GLN375 4.4 79.6 1.0
CA C:GLN375 4.5 54.7 1.0
ND2 C:ASN406 4.5 64.6 1.0
C C:PRO374 4.6 52.8 1.0
CA C:PRO374 4.6 52.1 1.0
CD C:GLN375 4.7 75.0 1.0
N C:ALA373 4.7 58.6 1.0
O C:LYS371 4.9 59.7 1.0
O C:HOH692 5.0 89.5 1.0

Chlorine binding site 7 out of 8 in 6pbz

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Chlorine binding site 7 out of 8 in the Crystal Structure of Escherichia Coli Gppa


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 Escherichia Coli Gppa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:77.5
occ:1.00
 N D:SER17 3.2 64.2 1.0
N D:ASN16 3.2 65.9 1.0
N D:SER15 3.6 58.4 1.0
CB D:ASN16 3.6 75.5 1.0
O D:SER17 3.7 57.8 1.0
CA D:ASN16 3.8 69.1 1.0
NE2 D:HIS19 3.8 58.0 1.0
CB D:SER17 3.9 63.2 1.0
C D:ASN16 3.9 66.7 1.0
CA D:SER17 4.0 61.6 1.0
CA D:GLY14 4.0 54.5 1.0
C D:GLY14 4.1 57.4 1.0
C D:SER15 4.2 62.4 1.0
C D:SER17 4.3 57.8 1.0
CA D:SER15 4.4 61.4 1.0
CD2 D:HIS19 4.6 57.6 1.0
CB D:SER15 4.7 65.4 1.0
CE1 D:HIS19 4.8 58.2 1.0
N D:GLY14 4.9 54.7 1.0
OG D:SER17 4.9 65.0 1.0

Chlorine binding site 8 out of 8 in 6pbz

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Chlorine binding site 8 out of 8 in the Crystal Structure of Escherichia Coli Gppa


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 Escherichia Coli Gppa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl502

b:0.5
occ:1.00
 CD D:ARG201 4.0 0.1 1.0
O D:TRP205 4.1 0.6 1.0
N D:TRP205 4.1 0.7 1.0
CE2 D:TRP205 4.1 0.4 1.0
CD2 D:TRP205 4.2 0.4 1.0
CZ2 D:TRP205 4.3 0.4 1.0
CH2 D:TRP205 4.4 0.7 1.0
CE3 D:TRP205 4.4 0.1 1.0
CA D:GLY204 4.5 0.9 1.0
CZ3 D:TRP205 4.5 0.3 1.0
NE1 D:TRP205 4.6 0.9 1.0
CG D:ARG201 4.7 0.6 1.0
CG D:TRP205 4.8 0.3 1.0
O D:ARG201 4.8 0.4 1.0
C D:GLY204 4.9 0.0 1.0
CD1 D:TRP205 5.0 0.7 1.0
C D:TRP205 5.0 0.2 1.0

Reference:

H.Song, M.N.Dharmasena, C.Wang, G.X.Shaw, S.Cherry, J.E.Tropea, D.J.Jin, X.Ji. Structure and Activity of Ppx/Gppa Homologs From Escherichia Coli and Helicobacter Pylori. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31679177
DOI: 10.1111/FEBS.15120
Page generated: Mon Jul 29 13:17:15 2024

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