Zinc in PDB 7kzz: Cryo-Em Structure of Yiip-Fab Complex in Holo State

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Yiip-Fab Complex in Holo State (pdb code 7kzz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of Yiip-Fab Complex in Holo State, PDB code: 7kzz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7kzz

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:93.9
occ:1.00
OD2 B:ASP287 1.7 67.8 1.0
NE2 B:HIS234 1.8 73.8 1.0
ND1 B:HIS250 1.9 71.2 1.0
CG B:HIS250 2.8 71.2 1.0
CD2 B:HIS234 2.8 73.8 1.0
CE1 B:HIS234 2.8 73.8 1.0
HB3 B:HIS250 2.9 71.2 1.0
CG B:ASP287 3.0 67.8 1.0
CE1 B:HIS250 3.0 71.2 1.0
HB2 B:HIS250 3.1 71.2 1.0
CB B:HIS250 3.1 71.2 1.0
HD2 B:HIS234 3.2 73.8 1.0
HE1 B:HIS234 3.2 73.8 1.0
HE1 B:HIS250 3.3 71.2 1.0
HB2 B:ASP287 3.7 67.8 1.0
OD1 B:ASP287 3.7 67.8 1.0
OD2 B:ASP235 3.8 76.9 1.0
HD2 B:HIS285 3.9 67.1 1.0
ND1 B:HIS234 3.9 73.8 1.0
CG B:HIS234 3.9 73.8 1.0
CB B:ASP287 3.9 67.8 1.0
CD2 B:HIS250 4.0 71.2 1.0
NE2 B:HIS250 4.0 71.2 1.0
HB3 B:ASP287 4.3 67.8 1.0
CA B:HIS250 4.6 71.2 1.0
CG B:ASP235 4.8 76.9 1.0
CD2 B:HIS285 4.8 67.1 1.0
HD1 B:HIS234 4.8 73.8 1.0
HB2 B:ASP235 4.9 76.9 1.0
HD2 B:HIS250 5.0 71.2 1.0
HE2 B:HIS250 5.0 71.2 1.0

Zinc binding site 2 out of 8 in 7kzz

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:127.8
occ:1.00
OD1 B:ASP70 1.7 104.4 1.0
OD2 B:ASP70 1.8 104.4 1.0
ND1 B:HIS73 1.9 98.9 1.0
NE2 B:HIS77 1.9 101.4 1.0
CG B:ASP70 2.2 104.4 1.0
HB2 B:HIS73 2.7 98.9 1.0
CG B:HIS73 2.8 98.9 1.0
CE1 B:HIS77 2.8 101.4 1.0
CD2 B:HIS77 3.0 101.4 1.0
CE1 B:HIS73 3.0 98.9 1.0
HE1 B:HIS77 3.1 101.4 1.0
CB B:HIS73 3.2 98.9 1.0
HD2 B:HIS77 3.3 101.4 1.0
HE1 B:HIS73 3.4 98.9 1.0
HB3 B:ASP72 3.5 100.7 1.0
CB B:ASP70 3.7 104.4 1.0
N B:HIS73 4.0 98.9 1.0
ND1 B:HIS77 4.0 101.4 1.0
H B:HIS73 4.0 98.9 1.0
CD2 B:HIS73 4.0 98.9 1.0
CG B:HIS77 4.0 101.4 1.0
HB3 B:HIS73 4.1 98.9 1.0
NE2 B:HIS73 4.1 98.9 1.0
HB3 B:ASP70 4.1 104.4 1.0
H B:ASP70 4.2 104.4 1.0
CA B:HIS73 4.2 98.9 1.0
HB2 B:ASP70 4.3 104.4 1.0
C B:ASP72 4.4 100.7 1.0
CB B:ASP72 4.6 100.7 1.0
OH B:TYR64 4.6 101.9 1.0
CA B:ASP70 4.6 104.4 1.0
H B:ASP72 4.6 100.7 1.0
N B:ASP70 4.7 104.4 1.0
O B:ASP70 4.7 104.4 1.0
C B:ASP70 4.9 104.4 1.0
HD1 B:HIS77 4.9 101.4 1.0
O B:ASP72 4.9 100.7 1.0
HD2 B:HIS73 5.0 98.9 1.0
CA B:ASP72 5.0 100.7 1.0
HA B:HIS73 5.0 98.9 1.0
O B:HIS73 5.0 98.9 1.0

Zinc binding site 3 out of 8 in 7kzz

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:158.1
occ:1.00
OD2 B:ASP51 1.7 119.8 1.0
OD1 B:ASP159 1.7 135.7 1.0
OD1 B:ASP47 1.8 119.3 1.0
OD2 B:ASP47 1.8 119.3 1.0
NE2 B:HIS155 2.0 137.6 1.0
CG B:ASP47 2.3 119.3 1.0
CG B:ASP159 2.9 135.7 1.0
CE1 B:HIS155 2.9 137.6 1.0
CG B:ASP51 3.0 119.8 1.0
HE1 B:HIS155 3.1 137.6 1.0
CD2 B:HIS155 3.2 137.6 1.0
OD2 B:ASP159 3.4 135.7 1.0
HD2 B:HIS155 3.5 137.6 1.0
OD1 B:ASP51 3.6 119.8 1.0
O B:ASP47 3.7 119.3 1.0
HA B:SER48 3.8 119.7 1.0
CB B:ASP47 3.8 119.3 1.0
HG B:SER48 3.8 119.7 1.0
HB2 B:ASP159 3.9 135.7 1.0
HD13 B:LEU162 4.0 125.5 1.0
C B:ASP47 4.0 119.3 1.0
CB B:ASP159 4.0 135.7 1.0
HB2 B:ASP51 4.1 119.8 1.0
ND1 B:HIS155 4.1 137.6 1.0
CB B:ASP51 4.1 119.8 1.0
CG B:HIS155 4.3 137.6 1.0
HB3 B:ASP47 4.3 119.3 1.0
HB2 B:ASP47 4.3 119.3 1.0
CA B:ASP47 4.5 119.3 1.0
N B:SER48 4.5 119.7 1.0
H B:ASP51 4.5 119.8 1.0
HB3 B:ASP159 4.6 135.7 1.0
HA B:ASP47 4.6 119.3 1.0
HD1 B:TYR156 4.6 142.8 1.0
CA B:SER48 4.6 119.7 1.0
HD22 B:ASN163 4.8 129.4 1.0
OG B:SER48 4.8 119.7 1.0
HB3 B:ASP51 4.9 119.8 1.0
CD1 B:LEU162 4.9 125.5 1.0
HA B:ASP159 5.0 135.7 1.0

Zinc binding site 4 out of 8 in 7kzz

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:105.1
occ:1.00
OD1 A:ASP287 1.8 67.3 1.0
OD2 B:ASP267 1.8 72.4 1.0
OD1 B:ASP267 1.8 72.4 1.0
NE2 B:HIS263 1.9 64.4 1.0
NE2 A:HIS285 2.0 66.9 1.0
CG B:ASP267 2.3 72.4 1.0
CE1 B:HIS263 2.8 64.4 1.0
CE1 A:HIS285 2.9 66.9 1.0
CD2 B:HIS263 3.0 64.4 1.0
HE1 A:HIS285 3.0 66.9 1.0
CG A:ASP287 3.1 67.3 1.0
HE1 B:HIS263 3.1 64.4 1.0
CD2 A:HIS285 3.2 66.9 1.0
HD2 B:HIS263 3.3 64.4 1.0
HD2 A:HIS285 3.5 66.9 1.0
HA A:ASP287 3.7 67.3 1.0
OD2 A:ASP287 3.8 67.3 1.0
CB B:ASP267 3.8 72.4 1.0
ND1 B:HIS263 4.0 64.4 1.0
CG B:HIS263 4.0 64.4 1.0
ND1 A:HIS285 4.1 66.9 1.0
HB2 B:ASP267 4.1 72.4 1.0
CB A:ASP287 4.2 67.3 1.0
CG A:HIS285 4.2 66.9 1.0
HB3 B:ASP267 4.4 72.4 1.0
CA A:ASP287 4.4 67.3 1.0
HD2 A:PRO288 4.5 65.4 1.0
HB3 A:ASP287 4.5 67.3 1.0
H B:ASP267 4.8 72.4 1.0
CA B:ASP267 4.8 72.4 1.0
HG22 B:THR266 4.8 65.9 1.0
HA B:ASP267 4.8 72.4 1.0
HD1 B:HIS263 4.9 64.4 1.0
N A:ASP287 4.9 67.3 1.0
HB B:THR266 4.9 65.9 1.0
N B:ASP267 4.9 72.4 1.0
HD1 A:HIS285 5.0 66.9 1.0

Zinc binding site 5 out of 8 in 7kzz

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:107.1
occ:1.00
OD1 B:ASP287 1.8 67.8 1.0
OD2 A:ASP267 1.8 72.8 1.0
OD1 A:ASP267 1.8 72.8 1.0
NE2 A:HIS263 1.9 64.5 1.0
NE2 B:HIS285 2.0 67.1 1.0
CG A:ASP267 2.3 72.8 1.0
CE1 A:HIS263 2.8 64.5 1.0
CE1 B:HIS285 2.9 67.1 1.0
CD2 A:HIS263 3.0 64.5 1.0
HE1 B:HIS285 3.0 67.1 1.0
CG B:ASP287 3.1 67.8 1.0
HE1 A:HIS263 3.1 64.5 1.0
CD2 B:HIS285 3.2 67.1 1.0
HD2 A:HIS263 3.3 64.5 1.0
HD2 B:HIS285 3.5 67.1 1.0
HA B:ASP287 3.7 67.8 1.0
OD2 B:ASP287 3.8 67.8 1.0
CB A:ASP267 3.8 72.8 1.0
ND1 A:HIS263 4.0 64.5 1.0
CG A:HIS263 4.0 64.5 1.0
ND1 B:HIS285 4.1 67.1 1.0
HB2 A:ASP267 4.1 72.8 1.0
CB B:ASP287 4.2 67.8 1.0
CG B:HIS285 4.2 67.1 1.0
HB3 A:ASP267 4.4 72.8 1.0
CA B:ASP287 4.4 67.8 1.0
HD2 B:PRO288 4.5 65.4 1.0
HB3 B:ASP287 4.5 67.8 1.0
H A:ASP267 4.8 72.8 1.0
HG22 A:THR266 4.8 66.1 1.0
CA A:ASP267 4.8 72.8 1.0
HA A:ASP267 4.8 72.8 1.0
HD1 A:HIS263 4.9 64.5 1.0
HB A:THR266 4.9 66.1 1.0
HD1 B:HIS285 4.9 67.1 1.0
N A:ASP267 4.9 72.8 1.0
N B:ASP287 5.0 67.8 1.0

Zinc binding site 6 out of 8 in 7kzz

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:95.0
occ:1.00
OD2 A:ASP287 1.7 67.3 1.0
NE2 A:HIS234 1.8 73.6 1.0
ND1 A:HIS250 1.9 70.6 1.0
CD2 A:HIS234 2.8 73.6 1.0
CG A:HIS250 2.8 70.6 1.0
CE1 A:HIS234 2.9 73.6 1.0
HB3 A:HIS250 2.9 70.6 1.0
CE1 A:HIS250 3.0 70.6 1.0
CG A:ASP287 3.0 67.3 1.0
HB2 A:HIS250 3.1 70.6 1.0
HD2 A:HIS234 3.1 73.6 1.0
CB A:HIS250 3.2 70.6 1.0
HE1 A:HIS234 3.3 73.6 1.0
HE1 A:HIS250 3.3 70.6 1.0
HB2 A:ASP287 3.7 67.3 1.0
OD1 A:ASP287 3.7 67.3 1.0
OD2 A:ASP235 3.8 76.8 1.0
HD2 A:HIS285 3.9 66.9 1.0
CG A:HIS234 3.9 73.6 1.0
CB A:ASP287 3.9 67.3 1.0
ND1 A:HIS234 3.9 73.6 1.0
CD2 A:HIS250 4.0 70.6 1.0
NE2 A:HIS250 4.0 70.6 1.0
HB3 A:ASP287 4.3 67.3 1.0
CA A:HIS250 4.7 70.6 1.0
CG A:ASP235 4.8 76.8 1.0
CD2 A:HIS285 4.8 66.9 1.0
HD1 A:HIS234 4.9 73.6 1.0
HB2 A:ASP235 4.9 76.8 1.0
HE2 A:HIS250 5.0 70.6 1.0
HD2 A:HIS250 5.0 70.6 1.0

Zinc binding site 7 out of 8 in 7kzz

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:128.2
occ:1.00
OD1 A:ASP72 1.8 101.3 1.0
OD1 A:ASP70 1.8 104.9 1.0
OD2 A:ASP70 1.8 104.9 1.0
ND1 A:HIS73 2.0 98.7 1.0
CG A:ASP70 2.2 104.9 1.0
NE2 A:HIS77 2.3 101.5 1.0
HB2 A:HIS73 2.8 98.7 1.0
CG A:HIS73 2.9 98.7 1.0
CG A:ASP72 3.0 101.3 1.0
CE1 A:HIS73 3.0 98.7 1.0
CE1 A:HIS77 3.2 101.5 1.0
CB A:HIS73 3.3 98.7 1.0
CD2 A:HIS77 3.3 101.5 1.0
HE1 A:HIS77 3.4 101.5 1.0
HE1 A:HIS73 3.4 98.7 1.0
H A:HIS73 3.5 98.7 1.0
OD2 A:ASP72 3.6 101.3 1.0
N A:HIS73 3.6 98.7 1.0
HD2 A:HIS77 3.7 101.5 1.0
H A:ASP72 3.7 101.3 1.0
CB A:ASP70 3.7 104.9 1.0
C A:ASP72 4.0 101.3 1.0
CD2 A:HIS73 4.1 98.7 1.0
CA A:HIS73 4.1 98.7 1.0
NE2 A:HIS73 4.1 98.7 1.0
CB A:ASP72 4.2 101.3 1.0
HB2 A:ASP70 4.2 104.9 1.0
HB3 A:ASP70 4.2 104.9 1.0
HB3 A:HIS73 4.3 98.7 1.0
H A:ASP70 4.3 104.9 1.0
ND1 A:HIS77 4.3 101.5 1.0
N A:ASP72 4.4 101.3 1.0
CA A:ASP72 4.4 101.3 1.0
CG A:HIS77 4.4 101.5 1.0
CA A:ASP70 4.6 104.9 1.0
HB2 A:ASP72 4.6 101.3 1.0
O A:ASP72 4.7 101.3 1.0
C A:ASP70 4.7 104.9 1.0
HD2 A:HIS71 4.7 103.6 1.0
N A:ASP70 4.8 104.9 1.0
O A:ASP70 4.8 104.9 1.0
HA A:HIS73 4.8 98.7 1.0

Zinc binding site 8 out of 8 in 7kzz

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of Yiip-Fab Complex in Holo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Yiip-Fab Complex in Holo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:156.4
occ:1.00
OD2 A:ASP51 1.7 118.9 1.0
OD1 A:ASP159 1.7 134.8 1.0
OD1 A:ASP47 1.8 118.4 1.0
OD2 A:ASP47 1.8 118.4 1.0
NE2 A:HIS155 2.0 137.1 1.0
CG A:ASP47 2.3 118.4 1.0
CG A:ASP159 2.9 134.8 1.0
CG A:ASP51 3.0 118.9 1.0
CE1 A:HIS155 3.0 137.1 1.0
CD2 A:HIS155 3.1 137.1 1.0
HE1 A:HIS155 3.2 137.1 1.0
HD2 A:HIS155 3.4 137.1 1.0
OD2 A:ASP159 3.5 134.8 1.0
OD1 A:ASP51 3.6 118.9 1.0
HG A:SER48 3.7 118.9 1.0
HA A:SER48 3.7 118.9 1.0
CB A:ASP47 3.8 118.4 1.0
O A:ASP47 3.8 118.4 1.0
HB2 A:ASP159 3.9 134.8 1.0
HD13 A:LEU162 3.9 124.9 1.0
HB2 A:ASP51 4.0 118.9 1.0
CB A:ASP159 4.0 134.8 1.0
C A:ASP47 4.1 118.4 1.0
CB A:ASP51 4.1 118.9 1.0
ND1 A:HIS155 4.1 137.1 1.0
CG A:HIS155 4.2 137.1 1.0
HB2 A:ASP47 4.3 118.4 1.0
HB3 A:ASP47 4.3 118.4 1.0
N A:SER48 4.4 118.9 1.0
CA A:ASP47 4.5 118.4 1.0
CA A:SER48 4.6 118.9 1.0
H A:ASP51 4.7 118.9 1.0
HB3 A:ASP159 4.7 134.8 1.0
OG A:SER48 4.7 118.9 1.0
HA A:ASP47 4.7 118.4 1.0
CD1 A:LEU162 4.8 124.9 1.0
HD1 A:TYR156 4.8 142.7 1.0
HB3 A:ASP51 4.8 118.9 1.0
HD12 A:LEU162 4.9 124.9 1.0
HA A:ASP159 4.9 134.8 1.0
HD22 A:ASN163 4.9 128.0 1.0
HD11 A:LEU162 5.0 124.9 1.0
H A:SER48 5.0 118.9 1.0

Reference:

M.L.Lopez-Redondo, S.Fan, A.Koide, S.Koide, O.Beckstein, D.L.Stokes. Cryo-Em Structure of Yiip-Fab Complex in Holo State To Be Published.
Page generated: Mon Jan 25 16:48:08 2021

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