Atomistry » Zinc » PDB 4xna-4y6q » 4xxo
Atomistry »
  Zinc »
    PDB 4xna-4y6q »
      4xxo »

Zinc in PDB 4xxo: Crystal Structure of Human APOBEC3A

Protein crystallography data

The structure of Crystal Structure of Human APOBEC3A, PDB code: 4xxo was solved by M.F.Bohn, S.M.D.Shandilya, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 2.84
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.752, 94.752, 213.962, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 25.3

Other elements in 4xxo:

The structure of Crystal Structure of Human APOBEC3A also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human APOBEC3A (pdb code 4xxo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Human APOBEC3A, PDB code: 4xxo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4xxo

Go back to Zinc Binding Sites List in 4xxo
Zinc binding site 1 out of 7 in the Crystal Structure of Human APOBEC3A


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 Human APOBEC3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:45.0
occ:1.00
O A:HOH321 2.2 35.9 1.0
ZN A:ZN202 3.2 58.7 1.0
OG1 A:THR31 3.7 43.8 1.0
O A:HOH306 4.0 33.8 1.0
ND1 A:HIS70 4.1 51.0 1.0
N A:CYS101 4.4 60.5 1.0
CB A:CYS101 4.5 66.8 1.0
O A:SER99 4.5 62.6 1.0
CE1 A:HIS70 4.5 50.2 1.0
SG A:CYS101 4.6 68.9 1.0
CG A:HIS70 4.6 40.7 1.0
CB A:THR31 4.6 42.6 1.0
CB A:TRP98 4.7 46.4 1.0
CD2 A:TYR130 4.8 63.0 1.0
CE2 A:TYR130 4.8 62.2 1.0
CA A:PRO100 4.8 55.9 1.0
CG2 A:THR31 4.9 42.2 1.0
CG A:TYR130 5.0 64.5 1.0
CZ A:TYR130 5.0 71.1 1.0
CB A:HIS70 5.0 40.1 1.0

Zinc binding site 2 out of 7 in 4xxo

Go back to Zinc Binding Sites List in 4xxo
Zinc binding site 2 out of 7 in the Crystal Structure of Human APOBEC3A


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 Human APOBEC3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:58.7
occ:1.00
ND1 A:HIS70 2.3 51.0 1.0
SG A:CYS106 2.4 56.1 1.0
SG A:CYS101 2.4 68.9 1.0
CE1 A:HIS70 3.1 50.2 1.0
CB A:CYS106 3.2 69.6 1.0
ZN A:ZN201 3.2 45.0 1.0
CG A:HIS70 3.3 40.7 1.0
CB A:CYS101 3.5 66.8 1.0
N A:CYS101 3.7 60.5 1.0
CB A:HIS70 3.7 40.1 1.0
O A:HOH321 3.9 35.9 1.0
CA A:CYS101 4.1 64.0 1.0
NE2 A:HIS70 4.2 53.6 1.0
CD2 A:HIS70 4.3 45.6 1.0
CA A:CYS106 4.4 67.9 1.0
N A:CYS106 4.5 65.3 1.0
C A:CYS101 4.7 67.4 1.0
C A:PRO100 4.8 60.9 1.0
O A:CYS101 4.8 64.8 1.0
CB A:TRP104 4.8 70.9 1.0
CA A:PRO100 5.0 55.9 1.0

Zinc binding site 3 out of 7 in 4xxo

Go back to Zinc Binding Sites List in 4xxo
Zinc binding site 3 out of 7 in the Crystal Structure of Human APOBEC3A


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 Human APOBEC3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:53.5
occ:1.00
NE2 A:HIS29 2.2 44.6 1.0
CL A:CL206 2.8 47.0 1.0
CD2 A:HIS29 3.2 47.6 1.0
CE1 A:HIS29 3.2 32.9 1.0
NZ A:LYS30 4.1 46.6 1.0
CE A:LYS30 4.2 63.6 1.0
ND1 A:HIS29 4.3 30.8 1.0
CG A:HIS29 4.3 39.2 1.0
O A:HOH324 4.5 57.2 1.0
CD A:LYS30 5.0 49.2 1.0

Zinc binding site 4 out of 7 in 4xxo

Go back to Zinc Binding Sites List in 4xxo
Zinc binding site 4 out of 7 in the Crystal Structure of Human APOBEC3A


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 Human APOBEC3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:41.1
occ:1.00
O A:HOH301 2.0 41.7 1.0
O A:HOH314 2.1 26.9 1.0
NE2 B:HIS56 2.3 30.3 1.0
NE2 A:HIS11 2.6 33.4 1.0
CE1 B:HIS56 2.9 35.0 1.0
CL B:CL203 3.2 41.5 1.0
CE1 A:HIS11 3.4 34.1 1.0
CD2 B:HIS56 3.5 39.9 1.0
CD2 A:HIS11 3.6 38.0 1.0
O B:HOH329 3.8 50.8 1.0
O A:HOH307 3.8 32.2 1.0
ND1 B:HIS56 4.2 31.6 1.0
O A:LEU12 4.2 45.8 1.0
O B:HOH307 4.4 35.7 1.0
O B:HOH310 4.4 46.0 1.0
CG B:HIS56 4.5 34.7 1.0
ND1 A:HIS11 4.6 37.3 1.0
N A:ASP14 4.6 34.7 1.0
CG A:HIS11 4.7 37.5 1.0
OD2 A:ASP14 4.7 47.0 1.0
CA A:MET13 4.7 33.5 1.0
CG A:ASP14 4.8 44.0 1.0
CZ A:PHE54 4.9 39.0 1.0

Zinc binding site 5 out of 7 in 4xxo

Go back to Zinc Binding Sites List in 4xxo
Zinc binding site 5 out of 7 in the Crystal Structure of Human APOBEC3A


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 Human APOBEC3A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:47.9
occ:1.00
NE2 A:HIS56 2.2 36.0 1.0
NE2 B:HIS11 2.2 38.7 1.0
O A:HOH316 2.4 18.5 1.0
CL B:CL203 2.6 41.5 1.0
CD2 A:HIS56 2.8 35.5 1.0
CE1 B:HIS11 3.0 40.5 1.0
CD2 B:HIS11 3.2 37.4 1.0
CE1 A:HIS56 3.3 41.6 1.0
O A:HOH307 3.7 32.2 1.0
O B:HOH307 3.8 35.7 1.0
CG A:HIS56 4.1 35.1 1.0
ND1 B:HIS11 4.2 37.1 1.0
ND1 A:HIS56 4.3 33.7 1.0
CG B:HIS11 4.3 40.8 1.0
O A:HOH301 4.3 41.7 1.0
O B:LEU12 4.5 39.0 1.0
CD1 B:ILE17 4.7 52.0 1.0
O A:HOH309 4.9 37.1 1.0
CE2 A:PHE54 4.9 32.6 1.0
OD1 B:ASP14 5.0 41.8 1.0

Zinc binding site 6 out of 7 in 4xxo

Go back to Zinc Binding Sites List in 4xxo
Zinc binding site 6 out of 7 in the Crystal Structure of Human APOBEC3A


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 Human APOBEC3A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:52.0
occ:1.00
ND1 B:HIS70 2.1 46.2 1.0
SG B:CYS101 2.3 60.2 1.0
SG B:CYS106 2.4 45.1 1.0
CE1 B:HIS70 2.9 47.4 1.0
ZN B:ZN202 3.1 44.1 1.0
CB B:CYS106 3.2 51.9 1.0
CG B:HIS70 3.2 49.2 1.0
CB B:CYS101 3.5 63.4 1.0
N B:CYS101 3.7 49.4 1.0
CB B:HIS70 3.7 46.4 1.0
NE2 B:HIS70 4.1 53.7 1.0
CA B:CYS101 4.1 56.6 1.0
CD2 B:HIS70 4.2 54.2 1.0
O B:HOH320 4.3 39.9 1.0
CB B:TRP104 4.4 68.5 1.0
CA B:CYS106 4.5 50.8 1.0
O B:HOH318 4.6 53.0 1.0
N B:CYS106 4.7 49.9 1.0
C B:PRO100 4.8 47.8 1.0
C B:CYS101 4.8 61.2 1.0
O B:HOH315 4.9 42.2 1.0
CA B:PRO100 4.9 50.8 1.0
O B:CYS101 5.0 57.8 1.0

Zinc binding site 7 out of 7 in 4xxo

Go back to Zinc Binding Sites List in 4xxo
Zinc binding site 7 out of 7 in the Crystal Structure of Human APOBEC3A


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 Human APOBEC3A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:44.1
occ:1.00
O B:HOH318 2.1 53.0 1.0
ZN B:ZN201 3.1 52.0 1.0
O B:HOH315 3.3 42.2 1.0
O B:HOH320 3.5 39.9 1.0
OG1 B:THR31 3.6 41.9 1.0
ND1 B:HIS70 3.8 46.2 1.0
CE1 B:HIS70 4.2 47.4 1.0
CG B:HIS70 4.3 49.2 1.0
N B:CYS101 4.4 49.4 1.0
SG B:CYS101 4.5 60.2 1.0
CB B:CYS101 4.6 63.4 1.0
CB B:THR31 4.6 35.6 1.0
O B:SER99 4.7 53.2 1.0
CB B:HIS70 4.7 46.4 1.0
CG2 B:THR31 4.7 36.4 1.0
CB B:TRP98 4.8 47.0 1.0
SG B:CYS106 4.8 45.1 1.0
NE2 B:HIS70 4.9 53.7 1.0
CE1 B:TYR130 4.9 56.0 1.0
CA B:PRO100 4.9 50.8 1.0
CD2 B:HIS70 4.9 54.2 1.0
CD1 B:TYR130 4.9 56.9 1.0
CZ B:TYR130 4.9 56.8 1.0

Reference:

M.F.Bohn, S.M.Shandilya, T.V.Silvas, E.A.Nalivaika, T.Kouno, B.A.Kelch, S.P.Ryder, N.Kurt-Yilmaz, M.Somasundaran, C.A.Schiffer. The Ssdna Mutator APOBEC3A Is Regulated By Cooperative Dimerization. Structure V. 23 903 2015.
ISSN: ISSN 0969-2126
PubMed: 25914058
DOI: 10.1016/J.STR.2015.03.016
Page generated: Wed Dec 16 05:55:50 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy