Atomistry » Zinc » PDB 4gsl-4gy0 » 4gsz
Atomistry »
  Zinc »
    PDB 4gsl-4gy0 »
      4gsz »

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

Go back to Zinc Binding Sites List in 4gsz
Zinc binding site 1 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 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

Go back to Zinc Binding Sites List in 4gsz
Zinc binding site 2 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 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

Go back to Zinc Binding Sites List in 4gsz
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

Go back to Zinc Binding Sites List in 4gsz
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

Go back to Zinc Binding Sites List in 4gsz
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

Go back to Zinc Binding Sites List in 4gsz
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

Go back to Zinc Binding Sites List in 4gsz
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

Go back to Zinc Binding Sites List in 4gsz
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

Go back to Zinc Binding Sites List in 4gsz
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: Sat Oct 26 23:30:43 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy