Zinc in PDB 7usf: Mouse Mammary Tumor Virus Strand Transfer Complex Intasome

Other elements in 7usf:

The structure of Mouse Mammary Tumor Virus Strand Transfer Complex Intasome also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Mouse Mammary Tumor Virus Strand Transfer Complex Intasome (pdb code 7usf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mouse Mammary Tumor Virus Strand Transfer Complex Intasome, PDB code: 7usf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7usf

Go back to Zinc Binding Sites List in 7usf
Zinc binding site 1 out of 4 in the Mouse Mammary Tumor Virus Strand Transfer Complex Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mouse Mammary Tumor Virus Strand Transfer Complex Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:107.5
occ:1.00
NE2 A:HIS9 2.0 93.8 1.0
ND1 A:HIS13 2.0 93.5 1.0
SG A:CYS37 2.3 101.4 1.0
SG A:CYS40 2.3 103.9 1.0
CE1 A:HIS9 2.7 93.8 1.0
CB A:CYS37 2.9 101.4 1.0
CE1 A:HIS13 2.9 93.5 1.0
CD2 A:HIS9 3.1 93.8 1.0
CG A:HIS13 3.1 93.5 1.0
CB A:HIS13 3.6 93.5 1.0
CB A:CYS40 3.7 103.9 1.0
ND1 A:HIS9 3.8 93.8 1.0
CG A:HIS9 4.0 93.8 1.0
CA A:HIS13 4.0 93.5 1.0
NE2 A:HIS13 4.1 93.5 1.0
N A:CYS40 4.1 103.9 1.0
CD2 A:HIS13 4.2 93.5 1.0
CA A:CYS40 4.3 103.9 1.0
CA A:CYS37 4.3 101.4 1.0
O A:HIS9 4.6 93.8 1.0
O A:VAL34 4.7 103.1 1.0
C A:HIS13 4.9 93.5 1.0
C A:CYS37 4.9 101.4 1.0
C A:ASN39 4.9 100.3 1.0
CG2 A:VAL34 5.0 103.1 1.0
O A:CYS37 5.0 101.4 1.0

Zinc binding site 2 out of 4 in 7usf

Go back to Zinc Binding Sites List in 7usf
Zinc binding site 2 out of 4 in the Mouse Mammary Tumor Virus Strand Transfer Complex Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mouse Mammary Tumor Virus Strand Transfer Complex Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:130.2
occ:1.00
ND1 B:HIS13 2.0 99.0 1.0
NE2 B:HIS9 2.1 103.9 1.0
SG B:CYS40 2.3 123.6 1.0
SG B:CYS37 2.3 121.1 1.0
CB B:CYS37 2.6 121.1 1.0
CE1 B:HIS13 2.7 99.0 1.0
CE1 B:HIS9 2.7 103.9 1.0
CD2 B:HIS9 3.1 103.9 1.0
CG B:HIS13 3.2 99.0 1.0
CB B:CYS40 3.6 123.6 1.0
CB B:HIS13 3.8 99.0 1.0
NE2 B:HIS13 3.8 99.0 1.0
ND1 B:HIS9 3.8 103.9 1.0
CG B:HIS9 4.0 103.9 1.0
CD2 B:HIS13 4.1 99.0 1.0
OD1 B:ASN39 4.1 122.5 1.0
CA B:CYS37 4.1 121.1 1.0
CA B:HIS13 4.5 99.0 1.0
O B:HIS9 4.6 103.9 1.0
O B:VAL34 4.7 120.3 1.0
CA B:CYS40 4.7 123.6 1.0
N B:CYS40 4.7 123.6 1.0
C B:CYS37 4.9 121.1 1.0
N B:CYS37 4.9 121.1 1.0

Zinc binding site 3 out of 4 in 7usf

Go back to Zinc Binding Sites List in 7usf
Zinc binding site 3 out of 4 in the Mouse Mammary Tumor Virus Strand Transfer Complex Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mouse Mammary Tumor Virus Strand Transfer Complex Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:236.6
occ:1.00
ND1 C:HIS13 2.0 190.9 1.0
NE2 C:HIS9 2.1 190.2 1.0
SG C:CYS40 2.3 204.9 1.0
SG C:CYS37 2.3 204.3 1.0
CE1 C:HIS9 2.9 190.2 1.0
CG C:HIS13 3.0 190.9 1.0
CE1 C:HIS13 3.0 190.9 1.0
CD2 C:HIS9 3.0 190.2 1.0
CB C:HIS13 3.3 190.9 1.0
CB C:CYS37 3.4 204.3 1.0
CB C:CYS40 3.6 204.9 1.0
CA C:HIS13 3.7 190.9 1.0
C C:ASN39 3.8 199.0 1.0
N C:CYS40 3.8 204.9 1.0
ND1 C:HIS9 3.9 190.2 1.0
O C:ASN39 4.0 199.0 1.0
CG C:HIS9 4.0 190.2 1.0
NE2 C:HIS13 4.1 190.9 1.0
CD2 C:HIS13 4.1 190.9 1.0
CA C:CYS40 4.1 204.9 1.0
CB C:ASN39 4.2 199.0 1.0
CA C:ASN39 4.3 199.0 1.0
N C:ASN39 4.4 199.0 1.0
O C:HIS9 4.5 190.2 1.0
CD C:LYS170 4.5 180.0 1.0
C C:HIS13 4.6 190.9 1.0
CA C:CYS37 4.7 204.3 1.0
O C:HIS13 4.8 190.9 1.0
N C:HIS13 4.9 190.9 1.0
C C:CYS37 4.9 204.3 1.0

Zinc binding site 4 out of 4 in 7usf

Go back to Zinc Binding Sites List in 7usf
Zinc binding site 4 out of 4 in the Mouse Mammary Tumor Virus Strand Transfer Complex Intasome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mouse Mammary Tumor Virus Strand Transfer Complex Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:222.0
occ:1.00
ND1 D:HIS13 2.0 172.5 1.0
NE2 D:HIS9 2.0 170.2 1.0
SG D:CYS40 2.3 187.2 1.0
SG D:CYS37 2.3 181.9 1.0
CE1 D:HIS9 2.5 170.2 1.0
CG D:HIS13 2.9 172.5 1.0
CB D:HIS13 3.1 172.5 1.0
CD2 D:HIS9 3.1 170.2 1.0
CE1 D:HIS13 3.1 172.5 1.0
CB D:CYS40 3.3 187.2 1.0
CB D:CYS37 3.5 181.9 1.0
ND1 D:HIS9 3.6 170.2 1.0
CA D:HIS13 3.7 172.5 1.0
CG D:HIS9 3.9 170.2 1.0
N D:CYS40 3.9 187.2 1.0
C D:ASN39 4.0 184.2 1.0
CD2 D:HIS13 4.1 172.5 1.0
CA D:CYS40 4.1 187.2 1.0
NE2 D:HIS13 4.1 172.5 1.0
CB D:ASN39 4.2 184.2 1.0
O D:ASN39 4.3 184.2 1.0
O D:HIS9 4.4 170.2 1.0
C D:HIS13 4.5 172.5 1.0
CA D:ASN39 4.6 184.2 1.0
O D:HIS13 4.7 172.5 1.0
N D:ASN39 4.8 184.2 1.0
N D:HIS13 4.8 172.5 1.0
CA D:CYS37 4.9 181.9 1.0

Reference:

I.K.Jozwik, W.Li, D.W.Zhang, D.Wong, J.Grawenhoff, A.Ballandras-Colas, S.Aiyer, P.Cherepanov, A.N.Engelman, D.Lyumkis. B-to-A Transition in Target Dna During Retroviral Integration. Nucleic Acids Res. V. 50 8898 2022.
ISSN: ESSN 1362-4962
PubMed: 35947647
DOI: 10.1093/NAR/GKAC644
Page generated: Sat Apr 8 04:28:58 2023

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