Chlorine in PDB 7jwf: Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose

Protein crystallography data

The structure of Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose, PDB code: 7jwf was solved by A.G.Hettle, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.517, 124.763, 142.423, 90.00, 93.86, 90.00
R / Rfree (%) 20.5 / 23.7

Other elements in 7jwf:

The structure of Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose also contains other interesting chemical elements:

Iodine (I) 120 atoms
Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose (pdb code 7jwf). 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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose, PDB code: 7jwf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 7jwf

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Chlorine binding site 1 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl748

b:62.1
occ:1.00
 O A:GLY240 3.7 68.3 1.0
O A:LEU237 3.7 59.5 1.0
CG2 A:VAL242 3.7 49.9 1.0
CB A:VAL242 3.8 49.2 1.0
CB A:LEU237 3.9 46.6 1.0
CB A:ASN238 4.1 55.9 1.0
C A:LEU237 4.1 58.6 1.0
N A:VAL242 4.4 48.5 1.0
CA A:LEU237 4.7 50.8 1.0
C A:GLY240 4.7 67.4 1.0
CA A:VAL242 4.7 45.3 1.0
N A:ASN238 4.8 58.4 1.0
CG1 A:VAL242 4.9 38.8 1.0
CD1 A:LEU237 5.0 40.3 1.0

Chlorine binding site 2 out of 10 in 7jwf

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Chlorine binding site 2 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl749

b:53.5
occ:1.00
 NZ A:LYS616 3.1 56.1 1.0
CG A:LYS576 3.6 44.1 1.0
CA A:LYS577 3.8 40.1 1.0
CB A:LYS577 4.0 43.1 1.0
N A:LYS577 4.0 40.2 1.0
C A:LYS576 4.2 39.5 1.0
O A:LYS576 4.2 43.1 1.0
CE A:LYS616 4.4 53.4 1.0
CB A:LYS576 4.6 46.0 1.0
CD A:LYS616 4.7 50.4 1.0

Chlorine binding site 3 out of 10 in 7jwf

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Chlorine binding site 3 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl750

b:36.1
occ:1.00
 O C:HOH894 3.2 32.5 1.0
ND2 C:ASN467 3.4 35.3 1.0
N A:SER606 3.5 40.6 1.0
CB A:SER606 3.5 39.7 1.0
CB C:ASN467 3.7 33.4 1.0
CE C:LYS443 3.9 42.8 1.0
CG C:ASN467 4.0 39.6 1.0
O C:HOH1019 4.1 46.1 1.0
N A:LYS605 4.1 36.9 1.0
CA A:SER606 4.1 37.2 1.0
CB C:LYS443 4.3 34.2 1.0
O A:HOH1102 4.4 45.2 1.0
CB A:LYS605 4.5 37.2 1.0
C A:LYS605 4.5 37.3 1.0
NZ C:LYS443 4.6 45.9 1.0
CA A:LYS605 4.6 35.5 1.0
O C:HOH1179 4.6 26.6 1.0
O C:HOH827 4.7 33.8 1.0
C A:GLY604 4.7 38.0 1.0
N C:GLY444 4.7 28.5 1.0
OG A:SER606 4.8 50.0 1.0
CA A:GLY604 4.8 39.0 1.0
CD C:LYS443 4.9 39.5 1.0
CG C:GLU466 4.9 32.9 1.0
O C:GLU466 4.9 30.1 1.0
OE2 C:GLU466 5.0 45.0 1.0

Chlorine binding site 4 out of 10 in 7jwf

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Chlorine binding site 4 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl745

b:51.6
occ:1.00
 ND2 B:ASN552 3.5 32.3 1.0
C2 B:EDO708 3.6 48.1 1.0
OD1 B:ASN552 3.7 34.2 1.0
OH B:TYR615 3.8 43.3 1.0
CZ B:TYR615 3.8 47.7 1.0
CE2 B:TYR615 4.0 47.5 1.0
O B:HOH951 4.0 37.3 1.0
O2 B:EDO708 4.0 63.1 1.0
CG B:ASN552 4.1 35.2 1.0
O1 B:EDO708 4.3 50.3 1.0
CG1 B:VAL583 4.3 40.9 1.0
CE1 B:TYR615 4.4 42.0 1.0
C1 B:EDO708 4.4 54.5 1.0
O B:HOH857 4.7 37.5 1.0
CD2 B:TYR615 4.7 46.6 1.0
CD B:LYS512 5.0 37.3 1.0

Chlorine binding site 5 out of 10 in 7jwf

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Chlorine binding site 5 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl746

b:50.9
occ:1.00
 O B:HOH1130 2.9 45.3 1.0
O B:HOH954 3.3 47.3 1.0
N B:LYS616 3.7 49.9 1.0
N B:TYR615 3.8 43.5 1.0
CB B:TYR615 3.9 43.8 1.0
CB B:THR614 3.9 48.0 1.0
OG1 B:THR614 4.1 47.3 1.0
CA B:TYR615 4.2 44.8 1.0
C B:TYR615 4.3 45.1 1.0
O B:LYS616 4.5 55.0 1.0
CA B:LYS616 4.5 50.7 1.0
CD2 B:TYR615 4.5 46.6 1.0
C B:THR614 4.7 44.0 1.0
CG B:TYR615 4.7 48.3 1.0
CA B:THR614 4.8 42.8 1.0
CG2 B:THR614 4.9 43.7 1.0
C B:LYS616 4.9 53.9 1.0

Chlorine binding site 6 out of 10 in 7jwf

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Chlorine binding site 6 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl747

b:44.0
occ:1.00
 OE2 B:GLU603 3.3 62.5 1.0
CE B:LYS547 3.3 57.2 1.0
N B:SER602 3.3 45.7 1.0
NZ B:LYS547 3.4 58.0 1.0
N B:GLU603 3.5 44.7 1.0
CG B:GLU603 3.7 54.6 1.0
CB B:SER602 3.8 47.9 1.0
CD B:GLU603 4.0 63.7 1.0
CA B:SER602 4.0 49.7 1.0
CB B:PHE601 4.1 43.6 1.0
CB B:GLU603 4.2 48.3 1.0
C B:SER602 4.2 48.6 1.0
CD2 B:PHE601 4.2 42.9 1.0
C B:PHE601 4.3 46.9 1.0
CA B:PHE601 4.3 40.7 1.0
CA B:GLU603 4.4 46.6 1.0
CD2 B:LEU608 4.5 50.4 1.0
CG B:PHE601 4.7 42.4 1.0
OG B:SER602 4.7 57.6 1.0
CD B:LYS547 4.8 46.5 1.0

Chlorine binding site 7 out of 10 in 7jwf

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Chlorine binding site 7 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl748

b:30.0
occ:1.00
 CG B:LYS538 3.8 39.2 1.0
CD B:LYS538 3.9 38.1 1.0
CA B:GLY539 4.0 32.2 1.0
N B:GLY539 4.1 33.9 1.0
CB B:LYS538 4.2 37.6 1.0
CE B:LYS538 4.2 32.4 1.0
C B:LYS538 4.3 37.2 1.0
O B:LYS538 4.5 37.4 1.0
CE B:LYS498 4.8 42.8 1.0
CA B:LYS538 4.9 35.1 1.0

Chlorine binding site 8 out of 10 in 7jwf

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Chlorine binding site 8 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl743

b:45.3
occ:1.00
 N C:ASN101 3.3 33.0 1.0
O C:HOH885 3.4 33.3 1.0
O C:ASN101 3.8 31.1 1.0
CA C:PHE100 3.8 33.1 1.0
CG C:LYS55 4.0 35.0 1.0
C C:PHE100 4.0 31.4 1.0
O C:SER99 4.1 33.5 1.0
ND2 C:ASN101 4.1 32.1 1.0
CA C:ASN101 4.2 33.1 1.0
CB C:ASN101 4.2 29.5 1.0
CA C:LYS55 4.2 35.5 1.0
CB C:LYS55 4.3 33.9 1.0
CE C:LYS55 4.4 34.1 1.0
C C:ASN101 4.5 28.6 1.0
CD2 C:PHE100 4.5 30.5 1.0
O C:HOH908 4.6 33.7 1.0
CB C:PHE100 4.6 30.2 1.0
CG C:ASN101 4.7 31.9 1.0
O C:LYS55 4.7 33.2 1.0
CD C:LYS55 4.7 32.2 1.0
CG C:PHE100 4.8 29.7 1.0
N C:PHE100 4.9 31.7 1.0
C C:SER99 4.9 33.0 1.0
C C:LYS55 5.0 33.4 1.0

Chlorine binding site 9 out of 10 in 7jwf

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Chlorine binding site 9 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl744

b:40.8
occ:1.00
 O2 G:GAL1 3.1 34.8 1.0
O C:HOH962 3.2 28.1 1.0
NH2 C:ARG265 3.2 25.9 1.0
NH2 C:ARG208 3.3 31.6 1.0
NZ C:LYS207 3.3 37.8 1.0
NH1 C:ARG208 3.3 32.4 1.0
O C:HOH1000 3.4 26.5 1.0
C2 G:GAL1 3.5 32.1 1.0
CZ C:ARG208 3.7 31.1 1.0
O1 G:GAL1 3.8 31.2 1.0
O C:HOH1045 3.9 34.9 1.0
CE C:LYS207 4.0 35.5 1.0
O C:HOH1148 4.1 38.3 1.0
ND2 C:ASN344 4.1 29.4 1.0
O C:HOH825 4.2 46.5 1.0
CZ C:ARG265 4.2 30.1 1.0
C1 G:GAL1 4.3 30.6 1.0
O C:HOH1135 4.4 38.0 1.0
NE C:ARG265 4.4 27.7 1.0
C3 G:GAL1 4.7 30.1 1.0
O3 G:GAL1 4.8 31.0 1.0
NE C:ARG208 4.9 32.9 1.0
NH1 C:ARG451 4.9 28.1 1.0

Chlorine binding site 10 out of 10 in 7jwf

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Chlorine binding site 10 out of 10 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl750

b:50.7
occ:1.00
 ND2 D:ASN552 3.4 30.3 1.0
CZ D:TYR615 3.7 40.5 1.0
OH D:TYR615 3.7 39.9 1.0
OD1 D:ASN552 3.7 33.1 1.0
CE2 D:TYR615 3.8 42.3 1.0
CG D:ASN552 4.0 33.4 1.0
O D:HOH1150 4.2 39.3 1.0
CE1 D:TYR615 4.2 31.6 1.0
CG1 D:VAL583 4.3 35.2 1.0
O D:HOH876 4.4 33.1 1.0
CD2 D:TYR615 4.5 40.4 1.0
O D:HOH1143 4.8 29.1 1.0
CD1 D:TYR615 4.8 34.9 1.0
O D:HOH912 4.9 34.1 1.0
CG D:TYR615 5.0 38.0 1.0

Reference:

B.E.Mcguire, A.Hettle, C.Vickers, D.T.King, D.J.Vocadlo, A.B.Boraston. The Structure of A Family 110 Glycoside Hydrolase Provides Insight Into the Hydrolysis of Alpha-(1,3)-Galactosidic Linkages in Lambda-Carrageenan and Blood Group Antigens. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33127644
DOI: 10.1074/JBC.RA120.015776
Page generated: Sun Dec 13 10:32:18 2020

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