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Zinc in PDB 3e2u: Crystal Structure of the Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued)

Protein crystallography data

The structure of Crystal Structure of the Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued), PDB code: 3e2u was solved by A.Weisbrich, S.Honnappa, G.Capitani, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.02 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 116.220, 116.310, 79.880, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued) (pdb code 3e2u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued), PDB code: 3e2u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3e2u

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Zinc binding site 1 out of 4 in the Crystal Structure of the Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued)


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 Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn102

b:53.8
occ:1.00
NE2 E:HIS1416 2.2 52.8 1.0
SG E:CYS1421 2.4 65.2 1.0
SG E:CYS1411 2.4 88.6 1.0
SG E:CYS1408 2.5 47.6 1.0
CB E:CYS1421 2.8 86.0 1.0
CE1 E:HIS1416 3.0 55.2 1.0
CB E:CYS1411 3.2 49.1 1.0
CD2 E:HIS1416 3.3 54.6 1.0
CB E:CYS1408 3.5 28.7 1.0
N E:CYS1411 3.7 72.0 1.0
O E:HOH96 3.8 60.6 1.0
CA E:CYS1421 3.9 62.2 1.0
CA E:CYS1411 4.0 66.4 1.0
ND1 E:HIS1416 4.2 44.5 1.0
CB E:ILE1410 4.3 51.6 1.0
CG E:HIS1416 4.3 46.9 1.0
CG2 D:ILE36 4.5 42.3 1.0
C E:ILE1410 4.6 70.5 1.0
N E:CYS1421 4.8 66.7 1.0
CG2 E:ILE1410 4.8 33.1 1.0
CA E:ILE1410 4.9 65.8 1.0
C E:CYS1421 4.9 66.0 1.0
CA E:CYS1408 4.9 75.0 1.0

Zinc binding site 2 out of 4 in 3e2u

Go back to Zinc Binding Sites List in 3e2u
Zinc binding site 2 out of 4 in the Crystal Structure of the Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued)


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 Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:66.0
occ:1.00
NE2 F:HIS1416 2.2 57.4 1.0
SG F:CYS1411 2.4 65.9 1.0
SG F:CYS1408 2.4 63.1 1.0
SG F:CYS1421 2.5 77.0 1.0
CB F:CYS1421 2.8 75.3 1.0
CE1 F:HIS1416 3.0 53.9 1.0
CD2 F:HIS1416 3.3 71.8 1.0
CB F:CYS1411 3.4 57.8 1.0
CB F:CYS1408 3.6 85.9 1.0
N F:CYS1411 3.7 74.1 1.0
CA F:CYS1421 3.8 58.8 1.0
O B:HOH117 3.8 38.0 1.0
CA F:CYS1411 4.1 68.4 1.0
ND1 F:HIS1416 4.2 50.7 1.0
CB F:ILE1410 4.2 53.9 1.0
CG F:HIS1416 4.3 34.3 1.0
CG2 C:ILE36 4.5 37.9 1.0
CG2 F:ILE1410 4.5 44.9 1.0
C F:ILE1410 4.5 73.6 1.0
C F:CYS1421 4.8 65.6 1.0
CA F:ILE1410 4.8 67.0 1.0
N F:CYS1421 4.8 64.6 1.0
CA F:CYS1408 5.0 72.2 1.0
N F:ILE1410 5.0 64.7 1.0

Zinc binding site 3 out of 4 in 3e2u

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Zinc binding site 3 out of 4 in the Crystal Structure of the Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued)


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 Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn103

b:74.6
occ:1.00
NE2 G:HIS1416 2.2 94.2 1.0
SG G:CYS1408 2.4 74.7 1.0
SG G:CYS1421 2.4 84.4 1.0
SG G:CYS1411 2.4 70.2 1.0
CE1 G:HIS1416 2.9 84.0 1.0
CB G:CYS1421 3.1 74.5 1.0
CB G:CYS1411 3.1 58.9 1.0
CB G:CYS1408 3.2 44.5 1.0
CD2 G:HIS1416 3.2 0.7 1.0
N G:CYS1411 3.7 73.1 1.0
ND1 G:HIS1416 4.0 89.1 1.0
CA G:CYS1411 4.0 67.8 1.0
CA G:CYS1421 4.0 61.9 1.0
CB G:ILE1410 4.1 71.8 1.0
CG G:HIS1416 4.2 96.2 1.0
CG2 G:ILE1410 4.3 64.7 1.0
CA G:CYS1408 4.6 68.4 1.0
C G:ILE1410 4.7 73.5 1.0
O C:HOH112 4.7 49.2 1.0
CG2 A:ILE36 4.9 61.7 1.0
CA G:ILE1410 4.9 61.5 1.0
N G:CYS1421 4.9 63.0 1.0
C G:CYS1408 5.0 67.8 1.0

Zinc binding site 4 out of 4 in 3e2u

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Zinc binding site 4 out of 4 in the Crystal Structure of the Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued)


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 Zink-Knuckle 2 Domain of Human Clip-170 in Complex with Cap-Gly Domain of Human Dynactin-1 (P150-Glued) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn104

b:70.9
occ:1.00
NE2 H:HIS1416 2.2 67.5 1.0
SG H:CYS1411 2.4 77.5 1.0
SG H:CYS1408 2.4 76.3 1.0
SG H:CYS1421 2.5 81.4 1.0
CE1 H:HIS1416 2.7 73.6 1.0
CB H:CYS1421 3.1 51.6 1.0
CB H:CYS1411 3.1 60.1 1.0
CB H:CYS1408 3.3 46.7 1.0
CD2 H:HIS1416 3.3 70.8 1.0
N H:CYS1411 3.7 71.0 1.0
ND1 H:HIS1416 3.9 79.5 1.0
CA H:CYS1411 4.0 64.0 1.0
CA H:CYS1421 4.0 60.5 1.0
CG H:HIS1416 4.2 64.4 1.0
CB H:ILE1410 4.2 68.9 1.0
CG2 H:ILE1410 4.6 63.5 1.0
CG2 B:ILE36 4.6 28.2 1.0
NE D:ARG90 4.6 81.9 1.0
C H:ILE1410 4.6 69.3 1.0
CA H:CYS1408 4.7 66.2 1.0
CA H:ILE1410 4.9 61.4 1.0
N H:CYS1421 4.9 64.5 1.0

Reference:

A.Weisbrich, S.Honnappa, R.Jaussi, O.Okhrimenko, D.Frey, I.Jelesarov, A.Akhmanova, M.O.Steinmetz. Structure-Function Relationship of Cap-Gly Domains Nat.Struct.Mol.Biol. V. 14 959 2007.
ISSN: ISSN 1545-9993
PubMed: 17828277
DOI: 10.1038/NSMB1291
Page generated: Wed Dec 16 04:14:41 2020

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