Zinc in PDB 8xmf: Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation.

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation. (pdb code 8xmf). 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 Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation., PDB code: 8xmf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8xmf

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation.


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 Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:165.2
occ:1.00
 SG B:CYS433 2.0 159.4 1.0
NE2 B:HIS370 2.0 130.5 1.0
OE2 B:GLU420 2.0 145.1 1.0
ND1 B:HIS387 2.1 124.3 1.0
CD B:GLU420 2.8 145.1 1.0
CB B:CYS433 2.8 159.4 1.0
OE1 B:GLU420 2.9 145.1 1.0
CD2 B:HIS370 2.9 130.5 1.0
CE1 B:HIS387 3.0 124.3 1.0
CE1 B:HIS370 3.1 130.5 1.0
CG B:HIS387 3.1 124.3 1.0
CB B:HIS387 3.4 124.3 1.0
CA B:CYS433 3.8 159.4 1.0
CG B:HIS370 4.1 130.5 1.0
NE2 B:HIS387 4.1 124.3 1.0
ND1 B:HIS370 4.1 130.5 1.0
CD2 B:HIS387 4.2 124.3 1.0
CG B:GLU420 4.2 145.1 1.0
C B:CYS433 4.6 159.4 1.0
N B:GLU434 4.8 151.1 1.0
CG B:GLU371 4.9 113.9 1.0
OE1 B:GLN418 4.9 122.8 1.0
CB B:GLU371 4.9 113.9 1.0
CA B:HIS387 4.9 124.3 1.0
O B:LEU435 4.9 145.0 1.0

Zinc binding site 2 out of 8 in 8xmf

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation.


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 Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:153.2
occ:1.00
 NE2 B:HIS373 2.0 92.7 1.0
OE1 B:GLU371 2.1 113.9 1.0
SG B:CYS447 2.3 125.7 1.0
SG B:CYS446 2.3 120.2 1.0
OE2 B:GLU371 2.4 113.9 1.0
CD B:GLU371 2.4 113.9 1.0
CE1 B:HIS373 2.8 92.7 1.0
O B:CYS446 2.9 120.2 1.0
CD2 B:HIS373 3.2 92.7 1.0
C B:CYS446 3.2 120.2 1.0
CB B:CYS446 3.4 120.2 1.0
CB B:CYS447 3.4 125.7 1.0
N B:CYS447 3.7 125.7 1.0
CG B:GLU371 3.8 113.9 1.0
CA B:CYS446 3.9 120.2 1.0
CA B:CYS447 4.0 125.7 1.0
ND1 B:HIS373 4.0 92.7 1.0
CG B:HIS373 4.2 92.7 1.0
C B:CYS447 4.3 125.7 1.0
CB B:GLU371 4.5 113.9 1.0
N B:CYS446 4.7 120.2 1.0
CA B:GLU371 4.7 113.9 1.0

Zinc binding site 3 out of 8 in 8xmf

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation.


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 Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:174.8
occ:1.00
 OD2 B:ASP47 2.0 130.4 1.0
OD1 B:ASP255 2.0 163.2 1.0
NE2 B:HIS251 2.0 171.6 1.0
NE2 B:HIS43 2.1 125.8 1.0
OD2 B:ASP255 2.3 163.2 1.0
CG B:ASP255 2.4 163.2 1.0
CD2 B:HIS251 2.4 171.6 1.0
CG B:ASP47 2.6 130.4 1.0
OD1 B:ASP47 2.7 130.4 1.0
CD2 B:HIS43 2.9 125.8 1.0
CE1 B:HIS43 3.0 125.8 1.0
CE1 B:HIS251 3.1 171.6 1.0
CG B:HIS251 3.6 171.6 1.0
ND1 B:HIS251 3.9 171.6 1.0
CB B:ASP255 3.9 163.2 1.0
O B:HIS251 3.9 171.6 1.0
CB B:ASP47 3.9 130.4 1.0
CG B:HIS43 4.0 125.8 1.0
ND1 B:HIS43 4.0 125.8 1.0
O B:HIS43 4.6 125.8 1.0
CA B:ASP255 4.6 163.2 1.0
C B:HIS251 4.6 171.6 1.0
N B:ASP255 4.7 163.2 1.0
CB B:HIS251 4.8 171.6 1.0

Zinc binding site 4 out of 8 in 8xmf

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation.


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 Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:147.7
occ:1.00
 SG A:CYS437 2.3 150.2 1.0
ND1 B:HIS408 2.5 129.8 1.0
ND1 B:HIS413 2.6 123.6 1.0
CB B:HIS413 3.0 123.6 1.0
CG B:HIS413 3.1 123.6 1.0
CA B:HIS413 3.3 123.6 1.0
CG B:HIS408 3.4 129.8 1.0
CB A:CYS437 3.4 150.2 1.0
CE1 B:HIS408 3.5 129.8 1.0
CB B:HIS408 3.5 129.8 1.0
CE1 B:HIS413 3.7 123.6 1.0
CA B:HIS408 4.0 129.8 1.0
O B:ILE412 4.0 112.9 1.0
O B:HIS413 4.1 123.6 1.0
C B:HIS413 4.2 123.6 1.0
CD2 B:HIS413 4.3 123.6 1.0
CA A:CYS437 4.3 150.2 1.0
N B:HIS413 4.4 123.6 1.0
CD2 B:HIS408 4.5 129.8 1.0
NE2 B:HIS408 4.5 129.8 1.0
NE2 B:HIS413 4.6 123.6 1.0
C B:ILE412 4.6 112.9 1.0
O B:HIS408 4.9 129.8 1.0
N B:HIS408 5.0 129.8 1.0
C B:HIS408 5.0 129.8 1.0

Zinc binding site 5 out of 8 in 8xmf

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation.


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 Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:155.4
occ:1.00
 CD2 A:HIS408 2.0 127.3 1.0
NE2 A:HIS408 2.0 127.3 1.0
ND1 A:HIS413 2.0 118.0 1.0
SG B:CYS437 2.4 147.8 1.0
CE1 A:HIS413 2.7 118.0 1.0
CG A:HIS413 3.0 118.0 1.0
CG A:HIS408 3.2 127.3 1.0
CE1 A:HIS408 3.3 127.3 1.0
CB B:CYS437 3.5 147.8 1.0
CB B:GLN440 3.6 140.8 1.0
CB A:HIS413 3.6 118.0 1.0
NE2 A:HIS413 3.8 118.0 1.0
ND1 A:HIS408 3.8 127.3 1.0
CA B:GLN440 3.9 140.8 1.0
CD2 A:HIS413 3.9 118.0 1.0
CA A:HIS413 4.0 118.0 1.0
O B:THR439 4.0 144.0 1.0
O A:HIS413 4.3 118.0 1.0
CB A:HIS408 4.4 127.3 1.0
OE1 B:GLN440 4.6 140.8 1.0
C A:HIS413 4.6 118.0 1.0
C B:THR439 4.7 144.0 1.0
N B:GLN440 4.8 140.8 1.0
O A:ILE412 4.8 112.0 1.0
CA B:CYS437 4.9 147.8 1.0
CA A:HIS408 4.9 127.3 1.0
CG B:GLN440 5.0 140.8 1.0

Zinc binding site 6 out of 8 in 8xmf

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation.


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 Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:164.0
occ:1.00
 OE2 A:GLU420 2.0 139.7 1.0
ND1 A:HIS387 2.0 121.8 1.0
NE2 A:HIS370 2.1 127.4 1.0
CB A:HIS387 2.2 121.8 1.0
SG A:CYS433 2.3 150.8 1.0
CE1 A:HIS370 2.3 127.4 1.0
CG A:HIS387 2.3 121.8 1.0
CD A:GLU420 2.9 139.7 1.0
CD2 A:HIS370 3.2 127.4 1.0
OE1 A:GLU420 3.2 139.7 1.0
CE1 A:HIS387 3.3 121.8 1.0
ND1 A:HIS370 3.4 127.4 1.0
CA A:HIS387 3.6 121.8 1.0
CD2 A:HIS387 3.7 121.8 1.0
CB A:CYS433 3.8 150.8 1.0
CG A:HIS370 3.8 127.4 1.0
O A:HIS387 3.9 121.8 1.0
NE2 A:HIS387 4.1 121.8 1.0
C A:HIS387 4.1 121.8 1.0
CG A:GLU420 4.3 139.7 1.0
O A:HIS370 4.3 127.4 1.0
CB A:GLU371 4.4 109.9 1.0
CA A:CYS433 4.5 150.8 1.0
N A:HIS387 4.6 121.8 1.0
C A:HIS370 4.9 127.4 1.0

Zinc binding site 7 out of 8 in 8xmf

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation.


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 Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:160.7
occ:1.00
 OE2 A:GLU371 2.0 109.9 1.0
NE2 A:HIS373 2.0 90.8 1.0
SG A:CYS447 2.3 131.9 1.0
SG A:CYS446 2.3 121.9 1.0
CE1 A:HIS373 2.4 90.8 1.0
O A:CYS446 2.8 121.9 1.0
CD A:GLU371 3.0 109.9 1.0
C A:CYS446 3.2 121.9 1.0
CD2 A:HIS373 3.4 90.8 1.0
CB A:CYS446 3.4 121.9 1.0
CB A:CYS447 3.4 131.9 1.0
OE1 A:GLU371 3.6 109.9 1.0
ND1 A:HIS373 3.7 90.8 1.0
N A:CYS447 3.7 131.9 1.0
CA A:CYS446 3.9 121.9 1.0
CA A:CYS447 4.0 131.9 1.0
CG A:GLU371 4.0 109.9 1.0
CG A:HIS373 4.2 90.8 1.0
C A:CYS447 4.3 131.9 1.0
N A:CYS446 4.6 121.9 1.0
CD1 B:PHE72 5.0 85.1 1.0
CE1 B:PHE72 5.0 85.1 1.0

Zinc binding site 8 out of 8 in 8xmf

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation.


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 Human ZNT1 Wt at A Low pH, in the Presence of Zinc, Determined in An Inward-Facing Conformation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:174.2
occ:1.00
 OD2 A:ASP47 2.0 130.8 1.0
OD2 A:ASP255 2.0 166.1 1.0
NE2 A:HIS43 2.0 121.7 1.0
NE2 A:HIS251 2.0 172.1 1.0
OD1 A:ASP255 2.1 166.1 1.0
CG A:ASP255 2.3 166.1 1.0
CE1 A:HIS43 2.3 121.7 1.0
CD2 A:HIS251 2.6 172.1 1.0
CG A:ASP47 2.6 130.8 1.0
OD1 A:ASP47 2.8 130.8 1.0
CE1 A:HIS251 3.0 172.1 1.0
CD2 A:HIS43 3.1 121.7 1.0
ND1 A:HIS43 3.4 121.7 1.0
CG A:HIS251 3.6 172.1 1.0
CB A:ASP255 3.8 166.1 1.0
ND1 A:HIS251 3.8 172.1 1.0
CG A:HIS43 3.8 121.7 1.0
CB A:ASP47 4.0 130.8 1.0
O A:HIS251 4.0 172.1 1.0
O A:HIS43 4.5 121.7 1.0
CA A:ASP255 4.6 166.1 1.0
N A:ASP255 4.7 166.1 1.0
C A:HIS251 4.8 172.1 1.0
CB A:HIS251 4.9 172.1 1.0

Reference:

Y.Long, Z.Zhu, Z.Zhou, C.Yang, Y.Chao, Y.Wang, Q.Zhou, M.W.Wang, Q.Qu. Structural Insights Into Human Zinc Transporter ZNT1 Mediated Zn 2+ Efflux. Embo Rep. 2024.
ISSN: ESSN 1469-3178
PubMed: 39390258
DOI: 10.1038/S44319-024-00287-3
Page generated: Wed Nov 13 13:47:31 2024

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