Zinc in PDB 7spd: Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group

Protein crystallography data

The structure of Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group, PDB code: 7spd was solved by Z.Xu, N.Schnicker, S.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.67 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.29, 114.12, 112.55, 90, 90, 90
R / Rfree (%) 21.2 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group (pdb code 7spd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group, PDB code: 7spd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7spd

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Zinc binding site 1 out of 6 in the Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group


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 Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:102.5
occ:1.00
ND1 A:HIS105 2.1 82.5 1.0
SG A:CYS132 2.3 95.0 1.0
SG A:CYS133 2.6 98.3 1.0
SG B:CYS111 2.8 96.6 1.0
CE1 A:HIS105 3.0 84.4 1.0
CG A:HIS105 3.2 75.6 1.0
CB B:CYS111 3.2 73.0 1.0
CB A:HIS105 3.6 78.2 1.0
CB A:CYS132 3.7 96.6 1.0
CA A:HIS105 3.8 79.7 1.0
O A:HIS105 3.9 94.2 1.0
N A:CYS133 4.1 90.6 1.0
CB A:CYS133 4.2 103.0 1.0
CB A:GLU130 4.2 83.1 1.0
NE2 A:HIS105 4.2 82.2 1.0
CD2 A:HIS105 4.3 78.2 1.0
C A:HIS105 4.4 80.4 1.0
C A:CYS132 4.4 92.6 1.0
CA A:CYS132 4.5 97.1 1.0
CA B:CYS111 4.7 71.8 1.0
CA A:CYS133 4.8 99.1 1.0
N A:CYS132 4.8 93.0 1.0
O A:GLU130 5.0 88.1 1.0

Zinc binding site 2 out of 6 in 7spd

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Zinc binding site 2 out of 6 in the Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group


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 Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:91.7
occ:0.71
NE2 A:HIS27 2.2 96.3 1.0
SG A:CYS29 2.3 93.4 1.0
CD2 A:HIS27 3.2 92.3 1.0
CE1 A:HIS27 3.3 98.6 1.0
CB A:CYS29 3.4 77.2 1.0
CA A:CYS29 4.2 73.5 1.0
CG A:HIS27 4.3 95.5 1.0
ND1 A:HIS27 4.4 100.8 1.0
N A:CYS29 5.0 82.5 1.0

Zinc binding site 3 out of 6 in 7spd

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Zinc binding site 3 out of 6 in the Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group


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 Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:118.3
occ:1.00
SG C:CYS133 2.0 115.9 1.0
ND1 C:HIS105 2.2 89.4 1.0
SG C:CYS132 2.3 105.0 1.0
SG D:CYS111 2.6 108.1 1.0
CG C:HIS105 3.1 82.5 1.0
CB D:CYS111 3.1 88.3 1.0
CE1 C:HIS105 3.3 84.8 1.0
CB C:HIS105 3.3 81.6 1.0
CB C:CYS133 3.5 96.1 1.0
CB C:CYS132 3.5 105.6 1.0
N C:CYS133 3.6 109.8 1.0
CA C:HIS105 4.2 74.1 1.0
C C:CYS132 4.2 110.7 1.0
CA C:CYS133 4.2 105.8 1.0
CD2 C:HIS105 4.3 78.2 1.0
NE2 C:HIS105 4.3 75.9 1.0
CA C:CYS132 4.4 104.8 1.0
CB C:GLU130 4.5 86.0 1.0
CA D:CYS111 4.7 86.7 1.0
N C:CYS132 4.8 103.7 1.0
N C:MET106 4.9 80.5 1.0

Zinc binding site 4 out of 6 in 7spd

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Zinc binding site 4 out of 6 in the Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group


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 Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:128.6
occ:1.00
ND1 D:HIS105 2.0 101.3 1.0
SG E:CYS111 2.2 108.3 1.0
SG D:CYS132 2.5 130.1 1.0
CE1 D:HIS105 2.8 97.0 1.0
O D:GLU130 3.0 106.5 1.0
CG D:HIS105 3.1 93.7 1.0
CB D:CYS132 3.1 115.9 1.0
N D:CYS132 3.2 110.5 1.0
CB E:CYS111 3.2 96.2 1.0
CB D:HIS105 3.6 88.6 1.0
CA D:CYS132 3.7 110.2 1.0
O D:CYS132 3.8 118.7 1.0
NE2 D:HIS105 4.0 91.3 1.0
CD2 D:HIS105 4.2 92.6 1.0
C D:GLU130 4.2 102.4 1.0
C D:SER131 4.2 109.3 1.0
C D:CYS132 4.3 116.0 1.0
CA D:HIS105 4.4 84.5 1.0
CA D:SER131 4.5 105.5 1.0
CA E:CYS111 4.6 98.6 1.0
N D:SER131 4.9 104.3 1.0
O D:LEU104 5.0 82.5 1.0

Zinc binding site 5 out of 6 in 7spd

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Zinc binding site 5 out of 6 in the Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group


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 Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn204

b:81.9
occ:0.50
SG D:CYS29 2.1 82.7 1.0
NE2 D:HIS27 2.4 83.4 1.0
CB D:CYS29 3.1 70.5 1.0
CE1 D:HIS27 3.2 82.0 1.0
CD2 D:HIS27 3.5 85.8 1.0
CA D:CYS29 4.3 69.0 1.0
ND1 D:HIS27 4.4 85.2 1.0
CG D:HIS27 4.6 84.2 1.0

Zinc binding site 6 out of 6 in 7spd

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Zinc binding site 6 out of 6 in the Crystal Structure of the Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group


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 Tetramerization Domain (29-147) From Human Voltage-Gated Potassium Channel KV2.1 in C 2 2 21 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:82.2
occ:0.73
NE2 E:HIS27 2.3 87.5 1.0
SG E:CYS29 2.4 97.4 1.0
CB E:CYS29 2.8 71.4 1.0
CE1 E:HIS27 3.0 90.0 1.0
CD2 E:HIS27 3.5 87.2 1.0
CA E:CYS29 4.0 71.2 1.0
ND1 E:HIS27 4.2 92.5 1.0
CG E:HIS27 4.5 87.7 1.0
O E:MET28 4.8 83.8 1.0
N E:CYS29 4.9 76.9 1.0

Reference:

Z.Xu, S.Khan, N.J.Schnicker, S.Baker. Pentameric Assembly of the KV2.1 Tetramerization Domain. Acta Crystallogr D Struct V. 78 792 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35647925
DOI: 10.1107/S205979832200568X
Page generated: Sat Apr 8 03:15:11 2023

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