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Zinc in PDB 6h3a: Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.

Enzymatic activity of Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.

All present enzymatic activity of Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.:
2.3.2.27; 3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain., PDB code: 6h3a was solved by J.A.Newman, H.Aitkenhead, M.Lim, H.L.Williams, J.Q.Svejstrup, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.98 / 5.51
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 299.914, 299.914, 299.914, 90.00, 90.00, 90.00
R / Rfree (%) 27.9 / 30.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain. (pdb code 6h3a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain., PDB code: 6h3a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6h3a

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Zinc binding site 1 out of 8 in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.


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 KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:0.3
occ:1.00
 SG A:CYS88 2.4 0.7 1.0
SG A:CYS68 2.4 0.3 1.0
SG A:CYS91 2.6 0.8 1.0
SG A:CYS65 2.9 0.0 1.0
CB A:CYS68 3.7 0.9 1.0
CB A:CYS65 3.8 1.0 1.0
CB A:CYS91 3.9 0.3 1.0
CB A:CYS88 4.0 0.3 1.0
N A:CYS91 4.2 0.6 1.0
N A:CYS68 4.3 0.9 1.0
CA A:CYS91 4.3 0.5 1.0
N A:CYS88 4.4 0.6 1.0
C A:ALA90 4.4 0.9 1.0
N A:GLY66 4.5 0.8 1.0
CA A:CYS68 4.6 0.4 1.0
O A:ALA90 4.6 0.9 1.0
O A:CYS88 4.6 0.1 1.0
CA A:CYS88 4.7 0.3 1.0
CB A:ALA90 4.8 0.4 1.0
N A:VAL67 5.0 0.9 1.0

Zinc binding site 2 out of 8 in 6h3a

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Zinc binding site 2 out of 8 in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.


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 KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:0.2
occ:1.00
 ND1 A:HIS85 2.2 0.5 1.0
SG A:CYS117 2.3 0.6 1.0
SG A:CYS83 2.5 0.0 1.0
CE1 A:HIS85 2.6 0.9 1.0
CB A:CYS120 2.8 1.0 1.0
N A:CYS120 3.0 0.7 1.0
CB A:CYS83 3.1 0.5 1.0
SG A:CYS120 3.3 0.1 1.0
CB A:CYS117 3.3 1.0 1.0
CG A:HIS85 3.3 0.7 1.0
CA A:CYS120 3.5 0.2 1.0
NE2 A:HIS85 3.7 0.1 1.0
CB A:VAL119 3.9 0.2 1.0
C A:VAL119 4.0 0.1 1.0
CB A:HIS85 4.1 0.1 1.0
CD2 A:HIS85 4.1 0.8 1.0
O A:CYS83 4.2 0.9 1.0
CA A:VAL119 4.3 0.6 1.0
N A:VAL119 4.3 0.8 1.0
CA A:CYS83 4.4 0.9 1.0
C A:CYS83 4.5 0.5 1.0
C A:CYS120 4.6 0.3 1.0
CA A:CYS117 4.7 0.6 1.0
CG1 A:VAL119 4.7 0.4 1.0
N A:HIS85 4.8 0.2 1.0
CG2 A:VAL119 4.8 1.0 1.0
N A:LYS121 4.9 0.4 1.0
NE2 F:HIS344 5.0 0.2 1.0

Zinc binding site 3 out of 8 in 6h3a

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Zinc binding site 3 out of 8 in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.


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 KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:0.7
occ:1.00
 SG A:CYS209 2.3 0.6 1.0
SG A:CYS229 2.3 0.3 1.0
ND1 A:HIS212 2.8 0.8 1.0
CB A:CYS209 3.2 0.2 1.0
CB A:CYS229 3.3 0.6 1.0
CG A:HIS212 3.6 0.8 1.0
SG A:CYS232 3.6 0.9 1.0
CB A:HIS212 3.7 0.4 1.0
CE1 A:HIS212 3.8 1.0 1.0
N A:CYS229 3.9 0.4 1.0
N A:HIS212 4.1 0.9 1.0
CA A:CYS229 4.1 0.2 1.0
O A:GLU215 4.3 0.6 1.0
CB A:CYS232 4.4 0.2 1.0
N A:CYS232 4.5 0.8 1.0
CA A:HIS212 4.5 0.3 1.0
C A:CYS229 4.7 0.3 1.0
CA A:CYS209 4.7 0.9 1.0
CB A:ASP231 4.8 0.2 1.0
CD2 A:HIS212 4.8 0.5 1.0
NE2 A:HIS212 4.9 0.8 1.0
O A:CYS229 4.9 0.8 1.0
N A:VAL211 4.9 0.3 1.0
OD2 A:ASP231 4.9 0.6 1.0

Zinc binding site 4 out of 8 in 6h3a

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Zinc binding site 4 out of 8 in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.


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 KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:0.5
occ:1.00
 ND1 A:HIS237 1.9 0.2 1.0
SG A:CYS221 2.3 0.5 1.0
SG A:CYS224 2.4 0.3 1.0
CE1 A:HIS237 2.6 0.1 1.0
CG A:HIS237 3.0 0.8 1.0
CB A:CYS224 3.1 0.9 1.0
ND1 A:HIS240 3.2 0.1 1.0
CB A:HIS237 3.6 0.1 1.0
N A:CYS224 3.7 0.1 1.0
C A:SER223 3.7 0.4 1.0
NE2 A:HIS237 3.8 0.7 1.0
CB A:CYS221 3.8 0.3 1.0
CB A:SER223 3.9 0.7 1.0
O A:SER223 3.9 0.2 1.0
CA A:CYS224 4.0 0.6 1.0
CE1 A:HIS240 4.0 0.5 1.0
CD2 A:HIS237 4.0 0.3 1.0
CG A:HIS240 4.2 0.5 1.0
CA A:SER223 4.2 0.8 1.0
CB A:HIS240 4.4 0.4 1.0
N A:SER223 4.5 1.0 1.0
CA A:HIS237 4.6 0.3 1.0
NE2 A:GLN233 4.8 0.9 1.0
CA A:CYS221 4.9 0.1 1.0
O A:CYS221 5.0 0.5 1.0
C A:CYS221 5.0 0.5 1.0

Zinc binding site 5 out of 8 in 6h3a

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Zinc binding site 5 out of 8 in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.


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 KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:0.0
occ:1.00
 SG F:CYS209 2.3 0.2 1.0
SG F:CYS229 2.4 0.6 1.0
ND1 F:HIS212 2.7 0.5 1.0
CB F:CYS209 3.2 0.9 1.0
SG F:CYS232 3.3 0.7 1.0
CB F:CYS229 3.4 0.9 1.0
CG F:HIS212 3.6 0.6 1.0
CE1 F:HIS212 3.6 0.7 1.0
N F:CYS229 3.7 0.7 1.0
CB F:CYS232 3.7 1.0 1.0
CB F:HIS212 3.8 0.1 1.0
N F:CYS232 4.0 0.6 1.0
CA F:CYS229 4.0 0.5 1.0
N F:HIS212 4.2 0.6 1.0
CA F:CYS232 4.4 0.0 1.0
C F:CYS229 4.5 0.5 1.0
CA F:HIS212 4.6 0.1 1.0
O F:CYS229 4.7 0.0 1.0
O F:GLU215 4.7 0.3 1.0
CA F:CYS209 4.7 0.6 1.0
NE2 F:HIS212 4.7 0.6 1.0
CD2 F:HIS212 4.7 0.2 1.0
CB F:ASP231 4.8 0.4 1.0
C F:THR228 4.8 0.8 1.0
N F:VAL211 4.9 0.9 1.0
N F:ASP231 4.9 0.7 1.0

Zinc binding site 6 out of 8 in 6h3a

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Zinc binding site 6 out of 8 in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.


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 KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:0.3
occ:1.00
 SG F:CYS221 2.1 0.3 1.0
ND1 F:HIS237 2.2 0.1 1.0
SG F:CYS224 2.4 0.5 1.0
CE1 F:HIS237 3.1 1.0 1.0
ND1 F:HIS240 3.2 0.2 1.0
CG F:HIS237 3.3 0.7 1.0
CB F:CYS224 3.5 0.1 1.0
CB F:HIS240 3.6 0.6 1.0
CB F:HIS237 3.6 0.0 1.0
CB F:CYS221 3.7 0.2 1.0
CG F:HIS240 3.8 0.7 1.0
CB F:SER223 3.9 0.3 1.0
N F:CYS224 3.9 0.3 1.0
C F:SER223 4.1 0.9 1.0
NE2 F:HIS237 4.2 0.6 1.0
CA F:CYS224 4.3 0.8 1.0
CD2 F:HIS237 4.3 0.3 1.0
CE1 F:HIS240 4.4 0.7 1.0
CA F:SER223 4.4 0.3 1.0
CA F:HIS237 4.4 0.2 1.0
O F:SER223 4.5 0.8 1.0
N F:SER223 4.6 0.5 1.0
NE2 F:GLN233 4.7 0.1 1.0
CA F:CYS221 4.8 0.9 1.0
CA F:HIS240 5.0 0.7 1.0
OG F:SER223 5.0 0.7 1.0
C F:CYS221 5.0 0.3 1.0

Zinc binding site 7 out of 8 in 6h3a

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Zinc binding site 7 out of 8 in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.


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 KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn503

b:0.8
occ:1.00
 SG F:CYS91 2.4 0.7 1.0
SG F:CYS68 2.5 0.2 1.0
SG F:CYS65 2.5 1.0 1.0
SG F:CYS88 2.7 0.8 1.0
CB F:CYS65 3.4 0.9 1.0
CB F:CYS68 3.8 0.9 1.0
CB F:CYS91 4.0 0.2 1.0
N F:CYS68 4.0 0.8 1.0
N F:GLY66 4.1 0.3 1.0
CB F:CYS88 4.1 0.4 1.0
N F:CYS88 4.3 0.7 1.0
CA F:CYS68 4.5 0.3 1.0
N F:VAL67 4.5 0.3 1.0
CA F:CYS65 4.7 0.8 1.0
CA F:CYS91 4.7 0.4 1.0
N F:CYS91 4.7 0.5 1.0
N F:ARG69 4.8 0.4 1.0
CA F:CYS88 4.8 0.4 1.0
CA F:GLY66 4.9 0.3 1.0
C F:CYS65 4.9 0.7 1.0
CB F:GLU70 5.0 0.3 1.0

Zinc binding site 8 out of 8 in 6h3a

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Zinc binding site 8 out of 8 in the Crystal Structure of the KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain.


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 KAP1 Rbcc Domain in Complex with the SMARCAD1 CUE1 Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn504

b:0.2
occ:1.00
 ND1 F:HIS85 2.0 0.7 1.0
CE1 F:HIS85 2.2 0.1 1.0
SG F:CYS117 2.5 0.8 1.0
CG F:HIS85 2.8 0.9 1.0
NE2 F:HIS85 2.9 0.3 1.0
SG F:CYS83 3.1 0.1 1.0
CB F:VAL119 3.2 0.1 1.0
CD2 F:HIS85 3.3 0.0 1.0
N F:CYS120 3.4 0.8 1.0
CB F:HIS85 3.8 0.3 1.0
CG2 F:VAL119 3.8 0.9 1.0
CB F:CYS120 3.9 0.1 1.0
CA F:VAL119 3.9 0.5 1.0
CG1 F:VAL119 4.0 0.3 1.0
N F:VAL119 4.0 0.7 1.0
C F:VAL119 4.1 1.0 1.0
CB F:CYS117 4.1 0.2 1.0
SG F:CYS120 4.1 0.2 1.0
CA F:CYS120 4.2 0.3 1.0
CB F:CYS83 4.2 0.6 1.0
O F:CYS83 4.8 1.0 1.0
N F:HIS85 4.9 0.4 1.0
CA F:HIS85 5.0 0.8 1.0
NE2 A:HIS344 5.0 0.8 1.0

Reference:

M.Lim, J.A.Newman, H.L.Williams, L.Masino, H.Aitkenhead, A.E.Gravard, O.Gileadi, J.Q.Svejstrup. A Ubiquitin-Binding Domain That Binds A Structural Fold Distinct From That of Ubiquitin. Structure V. 27 1316 2019.
ISSN: ISSN 0969-2126
PubMed: 31204252
DOI: 10.1016/J.STR.2019.05.003
Page generated: Mon Oct 28 22:20:48 2024

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