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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

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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

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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

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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

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