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Zinc in PDB 4gsz: Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex

Enzymatic activity of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex

All present enzymatic activity of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex, PDB code: 4gsz was solved by E.L.D'antonio, Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 91.121, 91.121, 69.772, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex (pdb code 4gsz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex, PDB code: 4gsz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4gsz

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Zinc binding site 1 out of 9 in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:39.3
occ:0.35
 OE1 B:GLU25 4.3 65.2 1.0
CD1 A:TYR188 4.8 37.6 1.0

Zinc binding site 2 out of 9 in 4gsz

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Zinc binding site 2 out of 9 in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:34.8
occ:1.00
 OD2 A:ASP124 2.1 38.6 1.0
ND1 A:HIS101 2.1 35.2 1.0
OD1 A:ASP128 2.1 33.6 1.0
O1 A:ABH405 2.2 34.6 1.0
OD2 A:ASP232 2.2 34.6 1.0
O2 A:ABH405 2.6 34.7 1.0
B A:ABH405 2.9 34.7 1.0
CE1 A:HIS101 3.0 36.3 1.0
CG A:ASP128 3.0 33.2 1.0
CG A:ASP124 3.1 37.1 1.0
CG A:HIS101 3.1 34.7 1.0
CG A:ASP232 3.2 34.0 1.0
OD2 A:ASP128 3.3 33.3 1.0
ZN A:ZN403 3.3 35.6 1.0
CB A:HIS101 3.5 35.5 1.0
CB A:ASP232 3.5 33.9 1.0
OD1 A:ASP124 3.5 38.3 1.0
O3 A:ABH405 3.6 36.4 1.0
NE2 A:HIS101 4.2 34.3 1.0
CE A:ABH405 4.2 33.5 1.0
CD2 A:HIS101 4.2 35.2 1.0
O A:HIS141 4.3 35.4 1.0
OD1 A:ASP232 4.3 34.2 1.0
NE1 A:TRP122 4.3 36.0 1.0
CB A:ASP124 4.4 34.2 1.0
CZ2 A:TRP122 4.4 36.1 1.0
CB A:ASP128 4.4 33.7 1.0
OD2 A:ASP234 4.6 38.3 1.0
CE2 A:TRP122 4.7 35.9 1.0
ZN A:ZN404 4.7 37.8 0.7
CA A:ASP232 4.9 32.4 1.0
CG A:GLU277 4.9 35.9 1.0
CA A:HIS101 5.0 37.7 1.0

Zinc binding site 3 out of 9 in 4gsz

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Zinc binding site 3 out of 9 in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:35.6
occ:1.00
 OD1 A:ASP124 2.2 38.3 1.0
OD2 A:ASP234 2.3 38.3 1.0
ND1 A:HIS126 2.3 32.7 1.0
O1 A:ABH405 2.4 34.6 1.0
OD1 A:ASP234 2.5 37.3 1.0
OD2 A:ASP232 2.5 34.6 1.0
CG A:ASP234 2.7 36.6 1.0
O3 A:ABH405 3.0 36.4 1.0
CG A:ASP124 3.0 37.1 1.0
OD2 A:ASP124 3.2 38.6 1.0
B A:ABH405 3.2 34.7 1.0
CE1 A:HIS126 3.2 34.2 1.0
ZN A:ZN402 3.3 34.8 1.0
CG A:ASP232 3.3 34.0 1.0
CG A:HIS126 3.4 34.0 1.0
CB A:HIS126 3.7 33.3 1.0
N A:HIS126 3.8 27.7 1.0
OD1 A:ASP232 3.9 34.2 1.0
N A:ALA125 4.0 28.6 1.0
OG1 A:THR246 4.1 32.1 1.0
O2 A:ABH405 4.1 34.7 1.0
CB A:ASP234 4.2 34.8 1.0
CB A:ASP232 4.2 33.9 1.0
OD2 A:ASP128 4.3 33.3 1.0
CB A:ASP124 4.3 34.2 1.0
CE A:ABH405 4.4 33.5 1.0
CA A:HIS126 4.4 31.5 1.0
CD A:ABH405 4.4 30.3 1.0
NE2 A:HIS126 4.4 32.8 1.0
CD2 A:HIS126 4.5 33.0 1.0
C A:ALA125 4.6 26.3 1.0
CA A:ASP124 4.7 32.4 1.0
O A:HOH504 4.7 35.6 1.0
OD1 A:ASP128 4.7 33.6 1.0
CA A:ALA125 4.7 27.1 1.0
CB A:ALA125 4.7 26.3 1.0
C A:ASP124 4.8 30.6 1.0
O A:THR246 4.8 35.8 1.0
O A:HIS126 4.9 34.1 1.0
CG A:ASP128 4.9 33.2 1.0

Zinc binding site 4 out of 9 in 4gsz

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Zinc binding site 4 out of 9 in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:37.8
occ:0.70
 ND1 A:HIS141 2.1 31.0 1.0
O A:HOH559 2.2 34.4 1.0
OE1 A:GLU277 2.2 38.7 1.0
O3 A:ABH405 2.4 36.4 1.0
O2 A:ABH405 2.5 34.7 1.0
CD A:GLU277 2.6 37.3 1.0
B A:ABH405 2.8 34.7 1.0
CE1 A:HIS141 2.9 31.5 1.0
CG A:HIS141 3.1 31.8 1.0
OE2 A:GLU277 3.2 38.5 1.0
CG A:GLU277 3.4 35.9 1.0
CE A:ABH405 3.5 33.5 1.0
CB A:HIS141 3.6 31.6 1.0
NE2 A:HIS141 4.0 32.6 1.0
O A:HOH504 4.0 35.6 1.0
OG1 A:THR246 4.0 32.1 1.0
O1 A:ABH405 4.1 34.6 1.0
CD2 A:HIS141 4.1 32.1 1.0
OD2 A:ASP232 4.4 34.6 1.0
CD A:ABH405 4.4 30.3 1.0
N A:HIS101 4.5 38.5 1.0
CB A:HIS101 4.5 35.5 1.0
CB A:GLU277 4.6 34.5 1.0
CG A:GLN19 4.6 44.7 1.0
ZN A:ZN402 4.7 34.8 1.0
OD2 A:ASP234 4.7 38.3 1.0
O A:HIS141 4.7 35.4 1.0
CA A:HIS141 4.9 33.9 1.0
CG2 A:THR246 4.9 30.8 1.0
C A:HIS141 4.9 34.9 1.0
CB A:ASP100 5.0 36.9 1.0

Zinc binding site 5 out of 9 in 4gsz

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Zinc binding site 5 out of 9 in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:38.4
occ:0.35
 ND1 A:HIS115 2.3 48.4 1.0
OD1 A:ASP117 2.6 53.2 1.0
O A:HOH560 2.8 49.0 1.0
CG A:HIS115 3.1 47.7 1.0
CB A:HIS115 3.2 47.3 1.0
O A:HOH557 3.4 47.0 1.0
CE1 A:HIS115 3.4 49.8 1.0
CG A:ASP117 3.5 53.4 1.0
CA A:HIS115 3.5 46.8 1.0
OD2 A:ASP117 3.6 55.8 1.0
CG A:PRO226 3.7 47.4 1.0
CD A:PRO226 3.8 47.5 1.0
C A:HIS115 4.2 45.8 1.0
CD2 A:HIS115 4.3 48.5 1.0
NE2 A:HIS115 4.4 49.2 1.0
O A:VAL114 4.6 47.8 1.0
N A:HIS115 4.7 46.4 1.0
CD A:PRO116 4.7 44.0 1.0
N A:PRO116 4.8 44.7 1.0
O A:HIS115 4.8 47.2 1.0
CB A:ASP117 4.9 49.4 1.0
N A:ASP117 4.9 47.1 1.0
CB A:PRO226 4.9 47.7 1.0

Zinc binding site 6 out of 9 in 4gsz

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Zinc binding site 6 out of 9 in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:38.6
occ:1.00
 OD1 B:ASP128 2.1 29.9 1.0
OD2 B:ASP124 2.1 30.7 1.0
ND1 B:HIS101 2.2 37.1 1.0
OD2 B:ASP232 2.2 33.9 1.0
O1 B:ABH403 2.3 39.5 1.0
O2 B:ABH403 2.5 40.5 1.0
B B:ABH403 2.9 40.1 1.0
CG B:ASP128 3.1 31.9 1.0
CG B:HIS101 3.1 37.9 1.0
CE1 B:HIS101 3.2 37.5 1.0
CG B:ASP232 3.2 34.0 1.0
CG B:ASP124 3.2 29.5 1.0
ZN B:ZN402 3.4 36.3 1.0
CB B:HIS101 3.4 38.0 1.0
OD2 B:ASP128 3.4 27.8 1.0
CB B:ASP232 3.5 35.3 1.0
O3 B:ABH403 3.6 40.1 1.0
OD1 B:ASP124 3.7 27.8 1.0
CE B:ABH403 4.2 40.6 1.0
NE1 B:TRP122 4.2 38.6 1.0
NE2 B:HIS101 4.3 37.4 1.0
CD2 B:HIS101 4.3 37.8 1.0
CZ2 B:TRP122 4.3 37.5 1.0
OD1 B:ASP232 4.3 32.6 1.0
CB B:ASP124 4.4 29.8 1.0
O B:HIS141 4.4 42.0 1.0
CB B:ASP128 4.4 32.4 1.0
OD2 B:ASP234 4.4 36.5 1.0
CE2 B:TRP122 4.6 38.2 1.0
ZN B:ZN404 4.7 29.6 0.4
OE1 B:GLU277 4.7 45.3 1.0
CG B:GLU277 4.8 41.8 1.0
CA B:ASP232 4.9 35.9 1.0
CA B:HIS101 4.9 40.2 1.0

Zinc binding site 7 out of 9 in 4gsz

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Zinc binding site 7 out of 9 in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:36.3
occ:1.00
 OD2 B:ASP234 2.2 36.5 1.0
OD1 B:ASP124 2.2 27.8 1.0
ND1 B:HIS126 2.2 32.6 1.0
O1 B:ABH403 2.3 39.5 1.0
OD1 B:ASP234 2.5 35.9 1.0
CG B:ASP234 2.6 35.4 1.0
OD2 B:ASP232 2.7 33.9 1.0
CE1 B:HIS126 3.0 34.1 1.0
O3 B:ABH403 3.0 40.1 1.0
CG B:ASP124 3.0 29.5 1.0
B B:ABH403 3.2 40.1 1.0
OD2 B:ASP124 3.2 30.7 1.0
CG B:ASP232 3.3 34.0 1.0
ZN B:ZN401 3.4 38.6 1.0
CG B:HIS126 3.4 33.9 1.0
OD1 B:ASP232 3.8 32.6 1.0
N B:HIS126 3.9 30.8 1.0
CB B:HIS126 3.9 31.3 1.0
N B:ALA125 4.0 31.1 1.0
O2 B:ABH403 4.1 40.5 1.0
OG1 B:THR246 4.1 44.8 1.0
CB B:ASP234 4.1 34.6 1.0
NE2 B:HIS126 4.2 33.9 1.0
CB B:ASP232 4.2 35.3 1.0
OD2 B:ASP128 4.2 27.8 1.0
CD B:ABH403 4.3 40.6 1.0
CE B:ABH403 4.3 40.6 1.0
CB B:ASP124 4.4 29.8 1.0
CD2 B:HIS126 4.4 33.8 1.0
CA B:HIS126 4.5 31.6 1.0
CB B:ALA125 4.5 29.8 1.0
OD1 B:ASP128 4.6 29.9 1.0
C B:ALA125 4.6 30.0 1.0
CA B:ALA125 4.6 30.1 1.0
O B:THR246 4.7 42.6 1.0
CA B:ASP124 4.7 31.4 1.0
C B:ASP124 4.8 31.8 1.0
CG B:ASP128 4.8 31.9 1.0

Zinc binding site 8 out of 9 in 4gsz

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Zinc binding site 8 out of 9 in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:29.6
occ:0.40
 ND1 B:HIS141 2.2 43.0 1.0
O3 B:ABH403 2.3 40.1 1.0
OE1 B:GLU277 2.3 45.3 1.0
O B:HOH538 2.4 41.9 1.0
CD B:GLU277 2.5 43.5 1.0
O2 B:ABH403 2.5 40.5 1.0
OE2 B:GLU277 2.7 44.4 1.0
B B:ABH403 2.8 40.1 1.0
CE1 B:HIS141 2.9 43.1 1.0
CG B:HIS141 3.2 42.9 1.0
CE B:ABH403 3.3 40.6 1.0
CG B:GLU277 3.5 41.8 1.0
CB B:HIS141 3.8 42.8 1.0
NE2 B:HIS141 4.0 43.0 1.0
O1 B:ABH403 4.0 39.5 1.0
OG1 B:THR246 4.0 44.8 1.0
CD2 B:HIS141 4.2 42.9 1.0
OD2 B:ASP232 4.3 33.9 1.0
CD B:ABH403 4.3 40.6 1.0
N B:HIS101 4.5 39.3 1.0
CB B:GLU277 4.5 41.0 1.0
OD2 B:ASP234 4.6 36.5 1.0
CB B:HIS101 4.6 38.0 1.0
ZN B:ZN401 4.7 38.6 1.0
O B:HOH537 4.7 33.7 1.0
O B:HIS141 4.7 42.0 1.0
NH2 B:ARG21 4.7 65.6 1.0
CB B:ASP100 4.8 40.0 1.0
CG B:GLN19 4.8 47.8 1.0
CA B:ASP100 4.9 39.9 1.0
CG2 B:THR246 5.0 42.6 1.0
C B:HIS141 5.0 41.8 1.0
CA B:HIS141 5.0 42.1 1.0

Zinc binding site 9 out of 9 in 4gsz

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Zinc binding site 9 out of 9 in the Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the ZN2+5-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:43.8
occ:0.35
 ND1 B:HIS115 2.2 59.5 1.0
O B:HOH543 2.4 42.4 1.0
OD1 B:ASP117 2.7 63.3 1.0
CG B:HIS115 3.0 59.0 1.0
CB B:HIS115 3.0 58.0 1.0
OD2 B:ASP117 3.0 64.8 1.0
CA B:HIS115 3.2 58.5 1.0
CG B:ASP117 3.3 62.4 1.0
CE1 B:HIS115 3.4 60.7 1.0
CG B:PRO226 4.1 47.8 1.0
C B:HIS115 4.1 58.7 1.0
O B:VAL114 4.2 58.7 1.0
CD2 B:HIS115 4.2 59.6 1.0
N B:HIS115 4.3 58.3 1.0
CD B:PRO226 4.4 47.9 1.0
NE2 B:HIS115 4.4 60.1 1.0
CD B:PRO116 4.4 58.3 1.0
N B:PRO116 4.6 58.5 1.0
C B:VAL114 4.7 58.2 1.0
CB B:ASP117 4.8 60.1 1.0
O B:HIS115 4.8 59.7 1.0

Reference:

E.L.D'antonio, Y.Hai, D.W.Christianson. Structure and Function of Non-Native Metal Clusters in Human Arginase I. Biochemistry V. 51 8399 2012.
ISSN: ISSN 0006-2960
PubMed: 23061982
DOI: 10.1021/BI301145N
Page generated: Wed Dec 16 05:20:36 2020

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