Atomistry » Zinc » PDB 5cvi-5d7w » 5cz2
Atomistry »
  Zinc »
    PDB 5cvi-5d7w »
      5cz2 »

Zinc in PDB 5cz2: Crystal Structure of A Two-Domain Fragment of Mmtv Integrase

Enzymatic activity of Crystal Structure of A Two-Domain Fragment of Mmtv Integrase

All present enzymatic activity of Crystal Structure of A Two-Domain Fragment of Mmtv Integrase:
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of A Two-Domain Fragment of Mmtv Integrase, PDB code: 5cz2 was solved by N.Cook, A.Ballandras-Colas, A.Engelman, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.57 / 2.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.370, 83.150, 141.140, 90.00, 90.19, 90.00
R / Rfree (%) 24.1 / 28

Other elements in 5cz2:

The structure of Crystal Structure of A Two-Domain Fragment of Mmtv Integrase also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase (pdb code 5cz2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase, PDB code: 5cz2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5cz2

Go back to Zinc Binding Sites List in 5cz2
Zinc binding site 1 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:55.8
occ:1.00
 ND1 G:HIS13 2.0 45.1 1.0
NE2 G:HIS9 2.0 55.6 1.0
SG G:CYS40 2.3 59.2 1.0
SG G:CYS37 2.3 51.4 1.0
CD2 G:HIS9 2.8 55.0 1.0
CG G:HIS13 2.9 50.0 1.0
CE1 G:HIS9 3.0 44.9 1.0
CE1 G:HIS13 3.1 56.1 1.0
CB G:HIS13 3.2 45.1 1.0
CB G:CYS37 3.4 52.9 1.0
CB G:CYS40 3.6 65.5 1.0
CA G:HIS13 3.7 43.8 1.0
CG G:HIS9 3.8 47.9 1.0
ND1 G:HIS9 3.9 44.3 1.0
CD2 G:HIS13 4.1 56.5 1.0
O G:HIS9 4.1 47.2 1.0
NE2 G:HIS13 4.1 56.3 1.0
N G:CYS40 4.4 68.0 1.0
CB G:ASN39 4.4 47.2 1.0
C G:ASN39 4.5 71.5 1.0
C G:HIS13 4.6 48.9 1.0
CA G:CYS40 4.6 68.6 1.0
O G:HIS13 4.8 53.8 1.0
N G:HIS13 4.8 43.2 1.0
CA G:CYS37 4.8 58.4 1.0
O G:ASN39 4.8 74.3 1.0
CA G:ASN39 4.8 48.0 1.0
N G:ASN39 4.9 59.7 1.0
CD A:LYS170 4.9 60.5 1.0
C G:HIS9 4.9 46.8 1.0

Zinc binding site 2 out of 6 in 5cz2

Go back to Zinc Binding Sites List in 5cz2
Zinc binding site 2 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:86.8
occ:1.00
 ND1 H:HIS13 2.0 63.3 1.0
NE2 H:HIS9 2.0 0.8 1.0
SG H:CYS40 2.3 97.6 1.0
SG H:CYS37 2.3 82.9 1.0
CD2 H:HIS9 2.8 0.2 1.0
CE1 H:HIS9 2.9 0.7 1.0
CG H:HIS13 3.0 56.8 1.0
CE1 H:HIS13 3.1 64.5 1.0
CB H:HIS13 3.3 62.1 1.0
CB H:CYS37 3.3 83.0 1.0
CB H:CYS40 3.7 97.3 1.0
CA H:HIS13 3.7 64.3 1.0
CG H:HIS9 3.9 94.5 1.0
ND1 H:HIS9 3.9 97.6 1.0
CD2 H:HIS13 4.1 55.4 1.0
NE2 H:HIS13 4.1 61.3 1.0
O H:HIS9 4.2 75.1 1.0
N H:CYS40 4.5 90.8 1.0
CB H:ASN39 4.5 64.5 1.0
C H:ASN39 4.6 81.2 1.0
C H:HIS13 4.6 65.7 1.0
CA H:CYS40 4.6 93.1 1.0
CA H:CYS37 4.7 83.0 1.0
O H:HIS13 4.8 70.2 1.0
N H:HIS13 4.8 64.3 1.0
O H:ASN39 4.9 75.7 1.0
CA H:ASN39 4.9 78.4 1.0
N H:ASN39 4.9 79.3 1.0
CD B:LYS170 5.0 62.5 1.0
C H:HIS9 5.0 73.8 1.0

Zinc binding site 3 out of 6 in 5cz2

Go back to Zinc Binding Sites List in 5cz2
Zinc binding site 3 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:83.9
occ:1.00
 NE2 I:HIS9 2.0 96.5 1.0
ND1 I:HIS13 2.0 64.8 1.0
SG I:CYS37 2.3 61.7 1.0
SG I:CYS40 2.3 88.8 1.0
CD2 I:HIS9 2.8 93.1 1.0
CE1 I:HIS9 2.9 95.7 1.0
CG I:HIS13 3.0 59.7 1.0
CE1 I:HIS13 3.0 68.4 1.0
CB I:HIS13 3.3 61.4 1.0
CB I:CYS37 3.4 62.2 1.0
CB I:CYS40 3.7 96.8 1.0
CA I:HIS13 3.8 62.5 1.0
CG I:HIS9 3.9 86.8 1.0
ND1 I:HIS9 3.9 90.2 1.0
CD2 I:HIS13 4.1 56.0 1.0
NE2 I:HIS13 4.1 63.4 1.0
O I:HIS9 4.2 63.8 1.0
CB I:ASN39 4.3 0.6 1.0
N I:CYS40 4.4 0.4 1.0
C I:ASN39 4.4 0.1 1.0
CA I:CYS40 4.6 0.6 1.0
C I:HIS13 4.7 65.2 1.0
CA I:ASN39 4.7 0.6 1.0
O I:ASN39 4.7 0.6 1.0
CA I:CYS37 4.8 72.5 1.0
N I:ASN39 4.8 0.2 1.0
O I:HIS13 4.9 72.5 1.0
CD F:LYS170 4.9 99.8 1.0
N I:HIS13 4.9 56.9 1.0

Zinc binding site 4 out of 6 in 5cz2

Go back to Zinc Binding Sites List in 5cz2
Zinc binding site 4 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:57.7
occ:1.00
 ND1 J:HIS13 2.0 68.9 1.0
NE2 J:HIS9 2.0 68.4 1.0
SG J:CYS40 2.3 89.7 1.0
SG J:CYS37 2.3 0.2 1.0
CD2 J:HIS9 2.8 67.8 1.0
CE1 J:HIS9 2.9 67.6 1.0
CG J:HIS13 2.9 68.2 1.0
CE1 J:HIS13 3.1 76.9 1.0
CB J:HIS13 3.2 71.0 1.0
CB J:CYS37 3.4 0.2 1.0
CB J:CYS40 3.6 94.2 1.0
CA J:HIS13 3.7 71.5 1.0
ND1 J:HIS9 3.8 66.5 1.0
CG J:HIS9 3.9 67.2 1.0
CD2 J:HIS13 4.1 68.2 1.0
NE2 J:HIS13 4.1 80.7 1.0
O J:HIS9 4.2 81.5 1.0
N J:CYS40 4.4 0.5 1.0
CB J:ASN39 4.4 84.4 1.0
C J:ASN39 4.4 0.2 1.0
CA J:CYS40 4.5 99.6 1.0
C J:HIS13 4.6 71.9 1.0
O J:HIS13 4.7 66.5 1.0
O J:ASN39 4.8 0.4 1.0
CA J:CYS37 4.8 0.9 1.0
CA J:ASN39 4.8 92.8 1.0
N J:HIS13 4.8 70.4 1.0
N J:ASN39 4.9 95.8 1.0
CD E:LYS170 4.9 65.8 1.0

Zinc binding site 5 out of 6 in 5cz2

Go back to Zinc Binding Sites List in 5cz2
Zinc binding site 5 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:64.2
occ:1.00
 NE2 K:HIS9 2.0 0.8 1.0
ND1 K:HIS13 2.0 86.1 1.0
SG K:CYS37 2.2 95.9 1.0
SG K:CYS40 2.3 83.8 1.0
CD2 K:HIS9 2.8 0.9 1.0
CE1 K:HIS9 2.9 0.6 1.0
CE1 K:HIS13 3.0 84.8 1.0
CG K:HIS13 3.0 84.1 1.0
CB K:CYS37 3.2 98.1 1.0
CB K:HIS13 3.4 84.8 1.0
CB K:CYS40 3.6 90.3 1.0
CG K:HIS9 3.9 0.8 1.0
CA K:HIS13 3.9 84.9 1.0
ND1 K:HIS9 3.9 0.6 1.0
NE2 K:HIS13 4.1 82.1 1.0
CD2 K:HIS13 4.2 82.2 1.0
O K:HIS9 4.2 89.9 1.0
N K:CYS40 4.3 90.3 1.0
CB K:ASN39 4.3 79.2 1.0
C K:ASN39 4.4 87.6 1.0
CA K:CYS40 4.5 93.5 1.0
CA K:CYS37 4.6 0.3 1.0
CA K:ASN39 4.7 84.6 1.0
N K:ASN39 4.7 90.1 1.0
O K:ASN39 4.8 87.6 1.0
C K:HIS13 4.8 80.9 1.0
O K:HIS13 4.9 78.5 1.0
N K:HIS13 5.0 78.8 1.0
C K:CYS37 5.0 0.8 1.0

Zinc binding site 6 out of 6 in 5cz2

Go back to Zinc Binding Sites List in 5cz2
Zinc binding site 6 out of 6 in the Crystal Structure of A Two-Domain Fragment of Mmtv Integrase


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 A Two-Domain Fragment of Mmtv Integrase within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn301

b:55.7
occ:1.00
 ND1 L:HIS13 2.0 40.7 1.0
NE2 L:HIS9 2.0 47.2 1.0
SG L:CYS37 2.3 88.8 1.0
SG L:CYS40 2.3 41.5 1.0
CD2 L:HIS9 2.8 45.6 1.0
CE1 L:HIS9 2.9 39.7 1.0
CG L:HIS13 3.0 40.1 1.0
CE1 L:HIS13 3.1 41.3 1.0
CB L:HIS13 3.2 39.5 1.0
CB L:CYS37 3.3 90.1 1.0
CB L:CYS40 3.6 52.9 1.0
CA L:HIS13 3.8 38.8 1.0
CG L:HIS9 3.9 45.5 1.0
ND1 L:HIS9 3.9 40.8 1.0
CD2 L:HIS13 4.1 53.1 1.0
NE2 L:HIS13 4.1 53.8 1.0
O L:HIS9 4.2 48.8 1.0
N L:CYS40 4.4 60.7 1.0
CB L:ASN39 4.4 54.5 1.0
C L:ASN39 4.4 61.4 1.0
CA L:CYS40 4.5 61.8 1.0
C L:HIS13 4.6 40.1 1.0
CA L:CYS37 4.7 88.0 1.0
O L:HIS13 4.8 38.7 1.0
CA L:ASN39 4.8 58.2 1.0
O L:ASN39 4.8 63.6 1.0
N L:ASN39 4.9 66.8 1.0
N L:HIS13 4.9 46.7 1.0
CD C:LYS170 4.9 45.3 1.0
C L:HIS9 5.0 45.4 1.0

Reference:

A.Ballandras-Colas, M.Brown, N.J.Cook, T.G.Dewdney, B.Demeler, P.Cherepanov, D.Lyumkis, A.N.Engelman. Cryo-Em Reveals A Novel Octameric Integrase Structure For Betaretroviral Intasome Function. Nature V. 530 358 2016.
ISSN: ESSN 1476-4687
PubMed: 26887496
DOI: 10.1038/NATURE16955
Page generated: Wed Dec 16 06:07:37 2020

Last articles

Cl in 6COG
Cl in 6CST
Cl in 6CTW
Cl in 6CTZ
Cl in 6CTT
Cl in 6CSP
Cl in 6CU9
Cl in 6CTX
Cl in 6CTU
Cl in 6CTP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy