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Zinc in PDB 4wwu: Structure of MEX67:MTR2

Protein crystallography data

The structure of Structure of MEX67:MTR2, PDB code: 4wwu was solved by S.Aibara, E.Valkov, M.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.65 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.610, 76.720, 199.120, 90.00, 94.09, 90.00
R / Rfree (%) 22.8 / 28.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of MEX67:MTR2 (pdb code 4wwu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of MEX67:MTR2, PDB code: 4wwu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4wwu

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Zinc binding site 1 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:18.4
occ:1.00
HE1 B:HIS128 1.6 36.8 1.0
OD2 B:ASP171 1.9 28.9 1.0
CE1 B:HIS128 2.1 30.7 1.0
NE2 B:HIS128 2.4 33.8 1.0
CG B:ASP171 2.9 37.7 1.0
OD1 B:ASP171 3.3 42.7 1.0
ND1 B:HIS128 3.4 37.6 1.0
CD2 B:HIS128 3.7 41.2 1.0
HD1 B:HIS128 3.9 45.2 1.0
CG B:HIS128 4.2 38.2 1.0
CB B:ASP171 4.2 43.8 1.0
HB3 B:ASP171 4.3 52.5 1.0
HD2 B:HIS128 4.4 49.5 1.0
HB1 B:ALA126 4.4 39.5 1.0
HB3 B:SER129 4.5 38.1 1.0
HB2 B:ASP171 4.6 52.5 1.0
HB2 B:ALA126 4.7 39.5 1.0
O B:ASP171 4.7 36.2 1.0
HA B:ALA126 4.8 40.8 1.0
CB B:ALA126 5.0 32.9 1.0

Zinc binding site 2 out of 12 in 4wwu

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Zinc binding site 2 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:51.2
occ:1.00
SG B:CYS194 2.4 28.1 1.0
OD1 B:ASN168 3.0 37.6 1.0
HB3 B:CYS194 3.1 36.6 1.0
HB2 B:CYS194 3.1 36.6 1.0
CB B:CYS194 3.2 30.5 1.0
HB2 B:ALA170 3.7 41.9 1.0
CG B:ASN168 3.8 31.3 1.0
HD12 B:LEU220 4.2 55.9 1.0
HD13 B:LEU220 4.3 55.9 1.0
HB2 B:ASN168 4.3 41.4 1.0
HD21 B:ASN168 4.4 37.7 1.0
ND2 B:ASN168 4.5 31.4 1.0
HB3 B:ALA170 4.5 41.9 1.0
HA B:ASN168 4.6 31.3 1.0
CB B:ALA170 4.6 34.9 1.0
CB B:ASN168 4.6 34.5 1.0
CA B:CYS194 4.7 24.3 1.0
CD1 B:LEU220 4.7 46.6 1.0
HB3 B:ALA196 4.9 34.7 1.0
HB1 B:ALA170 5.0 41.9 1.0
HB2 B:LEU220 5.0 35.3 1.0
HA B:CYS194 5.0 29.1 1.0

Zinc binding site 3 out of 12 in 4wwu

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Zinc binding site 3 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:60.7
occ:1.00
NE2 B:HIS374 2.0 56.7 1.0
OE1 B:GLU404 2.2 63.2 1.0
CE1 B:HIS374 2.6 65.5 1.0
HE1 B:HIS374 2.6 78.6 1.0
CD B:GLU404 2.8 62.9 1.0
OE2 B:GLU404 2.9 71.2 1.0
CD2 B:HIS374 3.2 64.7 1.0
HD2 B:HIS374 3.6 77.6 1.0
ND1 B:HIS374 3.9 68.5 1.0
HB2 B:GLU404 4.0 67.4 1.0
CG B:GLU404 4.1 59.4 1.0
CG B:HIS374 4.2 74.1 1.0
HG2 B:LYS372 4.3 80.0 1.0
HG3 B:GLU404 4.3 71.3 1.0
HB3 B:LYS372 4.4 78.2 1.0
CB B:GLU404 4.5 56.1 1.0
HD1 B:HIS374 4.6 82.2 1.0
HB3 B:GLU404 4.7 67.4 1.0
HG3 B:LYS372 4.7 80.0 1.0
HG2 B:GLU404 4.8 71.3 1.0
CG B:LYS372 4.8 66.6 1.0

Zinc binding site 4 out of 12 in 4wwu

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Zinc binding site 4 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:22.2
occ:1.00
HZ1 C:LYS25 1.5 29.8 1.0
NE2 C:HIS29 2.0 35.5 1.0
NZ C:LYS25 2.0 24.8 1.0
HZ3 C:LYS25 2.1 29.8 1.0
HE2 C:LYS25 2.2 64.1 1.0
CE C:LYS25 2.5 53.4 1.0
CE1 C:HIS29 2.7 42.5 1.0
HE1 C:HIS29 2.7 51.0 1.0
HZ2 C:LYS25 2.8 29.8 1.0
HE3 C:LYS25 2.9 64.1 1.0
HB3 L:ALA60 3.1 46.8 1.0
CD2 C:HIS29 3.2 31.9 1.0
HD2 C:HIS29 3.6 38.2 1.0
HD21 C:LEU44 3.8 54.6 1.0
HG2 L:GLN61 3.8 46.8 1.0
HD11 C:LEU44 3.9 38.7 1.0
CD C:LYS25 3.9 50.9 1.0
ND1 C:HIS29 3.9 32.5 1.0
HG21 L:VAL64 3.9 39.7 1.0
H L:ALA60 4.0 31.1 1.0
HG2 C:LYS25 4.0 56.3 1.0
CB L:ALA60 4.0 39.0 1.0
HB2 L:ALA60 4.0 46.8 1.0
HG3 C:LYS25 4.1 56.3 1.0
CG C:HIS29 4.1 31.3 1.0
CG C:LYS25 4.2 46.9 1.0
HD3 C:LYS25 4.2 61.0 1.0
H L:GLN61 4.3 36.7 1.0
HD2 C:LYS25 4.5 61.0 1.0
HB1 L:ALA60 4.5 46.8 1.0
HD1 C:HIS29 4.6 39.1 1.0
CD2 C:LEU44 4.7 45.5 1.0
CG L:GLN61 4.7 39.0 1.0
N L:ALA60 4.7 25.9 1.0
HG11 L:VAL64 4.7 38.0 1.0
CD1 C:LEU44 4.8 32.3 1.0
CG2 L:VAL64 4.8 33.1 1.0
HB L:VAL64 4.8 26.9 1.0
CA L:ALA60 4.9 29.9 1.0
N L:GLN61 5.0 30.6 1.0
HG23 L:VAL64 5.0 39.7 1.0

Zinc binding site 5 out of 12 in 4wwu

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Zinc binding site 5 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:0.6
occ:1.00
SG E:CYS194 2.3 32.1 1.0
OD1 E:ASN168 2.5 55.0 1.0
HB2 E:ALA170 2.9 59.4 1.0
HB3 E:CYS194 3.1 46.1 1.0
CB E:CYS194 3.3 38.4 1.0
CG E:ASN168 3.5 43.1 1.0
HB2 E:CYS194 3.6 46.1 1.0
CB E:ALA170 3.8 49.5 1.0
HB3 E:ALA170 3.8 59.4 1.0
HD21 E:ASN168 4.1 51.3 1.0
HB3 E:ALA196 4.1 43.6 1.0
HB1 E:ALA170 4.2 59.4 1.0
ND2 E:ASN168 4.2 42.8 1.0
H E:ALA170 4.3 45.1 1.0
HA E:ASN168 4.4 37.2 1.0
HB2 E:ASN168 4.5 48.7 1.0
CB E:ASN168 4.6 40.6 1.0
H E:ALA196 4.6 50.2 1.0
CA E:CYS194 4.7 32.1 1.0
HD22 E:LEU220 4.8 77.3 1.0
CA E:ALA170 4.9 36.8 1.0
N E:ALA170 4.9 37.6 1.0
HB2 E:ALA196 4.9 43.6 1.0
H E:LEU169 4.9 41.8 1.0
C E:CYS194 5.0 34.8 1.0
CB E:ALA196 5.0 36.3 1.0

Zinc binding site 6 out of 12 in 4wwu

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Zinc binding site 6 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:37.8
occ:1.00
HE1 E:HIS128 1.6 47.9 1.0
OD2 E:ASP171 1.9 46.6 1.0
CE1 E:HIS128 2.1 40.0 1.0
NE2 E:HIS128 2.3 38.6 1.0
CG E:ASP171 2.8 44.9 1.0
OD1 E:ASP171 3.1 42.4 1.0
ND1 E:HIS128 3.4 47.8 1.0
CD2 E:HIS128 3.7 43.2 1.0
HD1 E:HIS128 3.9 57.4 1.0
HB3 E:ASP171 4.0 49.9 1.0
CB E:ASP171 4.0 41.6 1.0
CG E:HIS128 4.2 42.5 1.0
O E:ASP171 4.3 47.6 1.0
HD2 E:HIS128 4.4 51.9 1.0
HB3 E:SER129 4.5 48.2 1.0
HB2 E:ASP171 4.5 49.9 1.0
HB1 E:ALA126 4.5 56.0 1.0
HA E:ALA126 4.7 45.9 1.0
HB2 E:ALA126 4.7 56.0 1.0

Zinc binding site 7 out of 12 in 4wwu

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Zinc binding site 7 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:10.7
occ:1.00
NE2 F:HIS29 2.1 24.9 1.0
HB3 I:ALA60 2.9 72.4 1.0
CE1 F:HIS29 3.0 30.5 1.0
HZ2 F:LYS25 3.1 50.4 1.0
HE1 F:HIS29 3.1 36.6 1.0
CD2 F:HIS29 3.2 23.9 1.0
HD2 F:HIS29 3.4 28.6 1.0
HB2 I:ALA60 3.4 72.4 1.0
H I:ALA60 3.5 40.3 1.0
CB I:ALA60 3.6 60.3 1.0
HD21 F:LEU44 3.6 52.3 1.0
HD11 F:LEU44 3.7 59.0 1.0
HD2 F:LYS25 3.7 49.4 1.0
HG21 I:VAL64 3.9 44.0 1.0
NZ F:LYS25 3.9 42.0 1.0
ND1 F:HIS29 4.1 23.9 1.0
HB1 I:ALA60 4.2 72.4 1.0
CG F:HIS29 4.2 25.2 1.0
HE3 F:LYS25 4.3 58.3 1.0
HZ1 F:LYS25 4.3 50.4 1.0
HB3 F:LYS25 4.3 37.8 1.0
N I:ALA60 4.3 33.6 1.0
HG11 I:VAL64 4.4 43.0 1.0
HZ3 F:LYS25 4.4 50.4 1.0
H I:GLN61 4.5 57.7 1.0
CE F:LYS25 4.5 48.6 1.0
CD F:LYS25 4.5 41.1 1.0
CD2 F:LEU44 4.6 43.5 1.0
CA I:ALA60 4.6 41.5 1.0
CD1 F:LEU44 4.6 49.1 1.0
HE21 I:GLN61 4.7 85.2 1.0
CG2 I:VAL64 4.9 36.7 1.0
HD1 F:HIS29 4.9 28.7 1.0
HD22 F:LEU44 4.9 52.3 1.0
HA I:PHE59 4.9 28.4 1.0
HG3 I:GLN61 4.9 69.7 1.0
HD13 F:LEU44 5.0 59.0 1.0

Zinc binding site 8 out of 12 in 4wwu

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Zinc binding site 8 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:81.5
occ:1.00
OE1 G:GLU56 2.1 94.3 1.0
ND1 G:HIS54 2.6 90.7 1.0
HG2 G:GLU56 2.8 98.6 1.0
HG3 G:GLU56 2.8 98.6 1.0
CE1 G:HIS54 2.8 0.4 1.0
CD G:GLU56 2.9 82.7 1.0
CG G:GLU56 3.0 82.2 1.0
HE1 G:HIS54 3.0 0.5 1.0
CG G:HIS54 3.1 88.1 1.0
NE2 G:HIS54 3.4 0.3 1.0
CD2 G:HIS54 3.6 95.4 1.0
HB2 G:HIS54 3.6 0.1 1.0
HE2 G:HIS54 3.9 0.2 1.0
CB G:HIS54 3.9 86.7 1.0
OE2 G:GLU56 4.1 72.3 1.0
HD2 G:HIS54 4.3 0.5 1.0
HB3 G:HIS54 4.3 0.1 1.0
HB G:ILE61 4.4 89.7 1.0
CB G:GLU56 4.5 79.0 1.0
HB2 G:GLU56 4.8 94.8 1.0
HB3 G:GLU56 4.9 94.8 1.0
HG13 G:ILE61 5.0 90.3 1.0

Zinc binding site 9 out of 12 in 4wwu

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Zinc binding site 9 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn501

b:54.5
occ:1.00
SG H:CYS194 2.3 62.2 1.0
HD22 H:LEU220 3.2 80.0 1.0
HB2 H:CYS194 3.3 77.5 1.0
CB H:CYS194 3.4 64.5 1.0
HB3 H:CYS194 3.5 77.5 1.0
OD1 H:ASN168 3.5 74.0 1.0
HB2 H:ALA170 3.6 94.5 1.0
HB3 H:ALA196 4.0 87.8 1.0
CD2 H:LEU220 4.0 66.7 1.0
HD23 H:LEU220 4.0 80.0 1.0
CB H:ALA170 4.4 78.8 1.0
HB2 H:ALA196 4.4 87.8 1.0
CG H:ASN168 4.5 72.2 1.0
HD21 H:LEU220 4.5 80.0 1.0
HB3 H:ALA170 4.5 94.5 1.0
HB1 H:ALA170 4.6 94.5 1.0
HB2 H:LEU220 4.6 73.3 1.0
CB H:ALA196 4.7 73.2 1.0
H H:ALA196 4.7 87.2 1.0
CA H:CYS194 4.8 54.9 1.0
HB3 H:LEU220 4.8 73.3 1.0
HD21 H:ASN168 4.8 79.3 1.0
HA H:CYS194 5.0 65.9 1.0

Zinc binding site 10 out of 12 in 4wwu

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Zinc binding site 10 out of 12 in the Structure of MEX67:MTR2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of MEX67:MTR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn501

b:80.1
occ:1.00
OE1 J:GLU56 2.6 82.7 1.0
HB3 J:HIS54 2.6 0.8 1.0
CG J:HIS54 3.1 0.2 1.0
CB J:HIS54 3.2 91.5 1.0
HB2 J:GLU56 3.2 0.8 1.0
CD2 J:HIS54 3.2 0.1 1.0
HB2 J:HIS54 3.3 0.8 1.0
HD2 J:HIS54 3.3 0.8 1.0
CD J:GLU56 3.7 85.4 1.0
HB J:ILE61 3.7 95.2 1.0
ND1 J:HIS54 3.7 0.3 1.0
NE2 J:HIS54 4.0 0.8 1.0
HG21 J:ILE61 4.0 0.8 1.0
CB J:GLU56 4.1 94.0 1.0
HG13 J:ILE61 4.2 84.7 1.0
CE1 J:HIS54 4.2 0.8 1.0
CG J:GLU56 4.3 93.3 1.0
HB3 J:GLU56 4.5 0.8 1.0
CB J:ILE61 4.5 79.3 1.0
HE2 J:HIS54 4.5 0.8 1.0
HG3 J:GLU56 4.5 0.0 1.0
CG2 J:ILE61 4.6 85.7 1.0
CA J:HIS54 4.6 86.2 1.0
OE2 J:GLU56 4.6 77.3 1.0
HG22 J:ILE61 4.7 0.8 1.0
CG1 J:ILE61 4.8 70.6 1.0
HE1 J:HIS54 4.9 0.5 1.0
HG12 J:ILE61 5.0 84.7 1.0

Reference:

S.Aibara, E.Valkov, M.Lamers, M.Stewart. Domain Organization Within the Nuclear Export Factor MEX67:MTR2 Generates An Extended Mrna Binding Surface. Nucleic Acids Res. 2015.
ISSN: ESSN 1362-4962
PubMed: 25618852
DOI: 10.1093/NAR/GKV030
Page generated: Wed Dec 16 05:51:55 2020

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