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Sodium in PDB 6quh: Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength

Protein crystallography data

The structure of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength, PDB code: 6quh was solved by T.Huyton, D.Gorlich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.16 / 1.50
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.476, 99.307, 102.011, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 21.9

Other elements in 6quh:

The structure of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 18 atoms
Copper (Cu) 6 atoms

Sodium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength (pdb code 6quh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength, PDB code: 6quh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in 6quh

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Sodium binding site 1 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na316

b:20.7
occ:0.99
 OG1 A:THR63 2.7 15.2 1.0
NH1 A:ARG96 2.9 15.7 1.0
OG1 A:THR108 2.9 13.9 1.0
CD A:ARG96 3.4 14.9 1.0
CG A:ARG96 3.5 16.0 1.0
CB A:ARG96 3.5 15.3 1.0
CB A:THR63 3.5 14.5 1.0
CA A:THR63 3.5 13.4 1.0
CG2 A:THR108 3.6 15.1 1.0
CD1 A:ILE98 3.7 15.5 1.0
CL A:CL312 3.7 24.0 0.6
CB A:THR108 3.7 13.1 1.0
CL A:CL309 3.9 22.2 0.6
CG2 A:THR63 3.9 15.5 1.0
CZ A:ARG96 3.9 17.3 1.0
N A:THR63 4.0 13.5 1.0
O A:HOH406 4.1 35.3 1.0
NE A:ARG96 4.1 17.7 1.0
O A:THR62 4.4 13.1 1.0
C A:THR62 4.4 10.7 1.0
CG1 A:ILE98 4.4 15.0 1.0
OG1 A:THR62 4.6 15.3 1.0
CA A:ARG96 4.7 14.3 1.0
O A:HOH412 4.8 17.9 1.0
C A:THR63 4.8 13.1 1.0
N A:ARG96 5.0 14.4 1.0

Sodium binding site 2 out of 11 in 6quh

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Sodium binding site 2 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na317

b:25.1
occ:1.00
 OE2 A:GLU17 2.8 24.3 1.0
O A:VAL29 2.8 15.8 1.0
C A:VAL29 3.5 15.7 1.0
CB A:GLU17 3.6 15.5 1.0
CD A:GLU17 3.6 16.1 1.0
CG A:GLU17 3.7 15.2 1.0
CA A:GLU17 4.0 14.7 1.0
N A:ARG30 4.1 15.4 1.0
CG A:ARG30 4.1 31.8 1.0
N A:LEU18 4.1 12.2 1.0
CA A:ARG30 4.1 15.5 1.0
CB A:ARG30 4.2 19.8 1.0
N A:VAL29 4.2 14.5 1.0
O A:LEU18 4.2 15.1 1.0
CB A:SER28 4.2 16.4 1.0
C A:GLU17 4.5 13.9 1.0
OG1 A:THR49 4.5 16.6 1.0
CA A:VAL29 4.5 16.6 1.0
CG2 A:THR49 4.6 16.8 1.0
OE1 A:GLU17 4.7 17.0 1.0
CD A:ARG30 4.7 28.9 1.0
C A:SER28 4.8 14.5 1.0
OG A:SER28 4.9 18.4 1.0
OD1 A:ASP19 4.9 18.8 1.0
C A:LEU18 4.9 14.4 1.0

Sodium binding site 3 out of 11 in 6quh

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Sodium binding site 3 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na318

b:22.4
occ:0.86
 OH A:TYR92 2.6 19.3 1.0
O3 A:CRO66 2.6 15.9 1.0
OE1 A:GLN94 2.7 16.3 1.0
N A:GLN69 2.9 13.5 1.0
C3 A:CRO66 3.1 16.3 1.0
CZ A:TYR92 3.4 17.2 1.0
CE1 A:TYR92 3.4 16.6 1.0
CA A:VAL68 3.5 16.0 1.0
CD A:GLN94 3.6 14.2 1.0
N A:VAL68 3.6 17.0 1.0
C A:VAL68 3.7 13.8 1.0
CB A:GLN69 3.8 16.0 1.0
NE2 A:GLN94 3.9 14.9 1.0
CA A:GLN69 3.9 14.3 1.0
CG A:GLN69 4.1 17.5 1.0
O2 A:CRO66 4.1 15.1 1.0
OE1 A:GLN69 4.2 17.0 1.0
CA3 A:CRO66 4.2 15.7 1.0
CG2 A:VAL112 4.2 14.7 1.0
CL A:CL308 4.2 20.1 0.6
OD1 A:ASN185 4.5 18.1 1.0
CD A:GLN69 4.5 16.8 1.0
N A:CYS70 4.6 14.4 1.0
CD1 A:PHE84 4.6 15.6 1.0
C A:GLN69 4.7 14.8 1.0
CE2 A:TYR92 4.7 16.2 1.0
CD1 A:TYR92 4.7 16.6 1.0
CE1 A:PHE84 4.7 15.5 1.0
CG1 A:VAL112 4.7 15.9 1.0
C2 A:CRO66 4.8 12.3 1.0
CG A:GLN94 4.8 15.0 1.0
N3 A:CRO66 4.8 12.1 1.0
CB A:VAL112 4.9 13.8 1.0
CB A:GLN94 4.9 15.0 1.0
CB A:VAL68 4.9 14.0 1.0
O A:VAL68 4.9 14.3 1.0

Sodium binding site 4 out of 11 in 6quh

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Sodium binding site 4 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na319

b:26.0
occ:0.81
 CG2 A:THR186 2.6 23.1 0.5
OE1 A:GLU95 2.7 28.0 1.0
CG2 A:THR186 2.8 13.1 0.5
O A:GLN184 3.1 17.5 1.0
O A:VAL93 3.3 17.8 1.0
OG1 A:THR186 3.5 23.9 0.5
N A:THR186 3.5 19.3 0.5
N A:THR186 3.5 18.3 0.5
C A:GLN184 3.5 15.7 1.0
CD A:GLU95 3.6 24.9 1.0
CG A:GLN184 3.6 26.2 1.0
CB A:THR186 3.6 15.7 0.5
CA A:ASN185 3.8 15.8 1.0
C A:ASN185 3.8 16.3 1.0
CG A:GLU95 3.8 20.1 1.0
N A:ASN185 3.8 16.2 1.0
CG1 A:VAL93 3.9 19.8 1.0
CB A:THR186 3.9 24.3 0.5
C A:VAL93 4.0 14.0 1.0
N A:GLU95 4.1 15.7 1.0
NE2 A:GLN184 4.2 35.2 1.0
CB A:GLU95 4.2 16.8 1.0
CB A:VAL93 4.2 15.9 1.0
CA A:THR186 4.2 15.4 0.5
CB A:GLN184 4.2 19.6 1.0
CA A:THR186 4.3 20.0 0.5
CD A:GLN184 4.3 29.0 1.0
CA A:GLN184 4.5 16.3 1.0
N A:GLN94 4.6 14.3 1.0
CA A:GLN94 4.6 15.4 1.0
O A:ASN185 4.7 17.6 1.0
OE2 A:GLU95 4.7 32.7 1.0
C A:GLN94 4.7 15.4 1.0
NH1 A:ARG158 4.7 88.3 1.0
CA A:VAL93 4.7 15.5 1.0
CA A:GLU95 4.8 15.4 1.0
OG1 A:THR186 5.0 25.0 0.5

Sodium binding site 5 out of 11 in 6quh

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Sodium binding site 5 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na320

b:28.4
occ:0.97
 O A:SER86 2.7 13.7 1.0
O A:MET88 2.8 16.2 1.0
NH1 A:ARG3 2.9 20.5 1.0
CD A:ARG3 3.6 19.6 1.0
C A:SER86 3.6 13.4 1.0
N A:GLY4 3.6 15.7 1.0
CG A:ARG3 3.8 15.7 1.0
CB A:ARG3 3.8 17.9 1.0
C A:MET88 3.8 15.3 1.0
O A:HOH483 3.8 17.8 1.0
CZ A:ARG3 3.9 19.5 1.0
N A:MET88 4.0 16.7 1.0
CA A:GLY4 4.0 15.6 1.0
NE A:ARG3 4.2 17.9 1.0
C A:ALA87 4.3 15.6 1.0
CA A:SER86 4.3 15.9 1.0
O A:LYS85 4.4 15.7 1.0
C A:ARG3 4.4 16.1 1.0
N A:ALA87 4.4 16.7 1.0
O A:HOH545 4.5 20.8 1.0
OE1 A:GLU90 4.5 17.6 1.0
CA A:MET88 4.5 14.8 1.0
CA A:ARG3 4.6 17.1 1.0
CA A:ALA87 4.7 13.5 1.0
O A:HOH560 4.8 17.5 1.0
N A:PRO89 4.8 15.8 1.0
O A:ALA87 4.9 17.1 1.0
CD A:PRO89 5.0 16.9 1.0

Sodium binding site 6 out of 11 in 6quh

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Sodium binding site 6 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na321

b:32.1
occ:0.88
 O A:ILE123 2.9 15.4 1.0
O A:HOH445 3.1 25.9 1.0
O A:GLU17 3.3 16.2 1.0
N A:ILE123 3.6 13.3 1.0
C A:ILE123 3.7 15.5 1.0
OD2 A:ASP19 3.7 18.4 1.0
C A:GLU17 3.8 13.9 1.0
N A:ASP19 3.8 13.8 1.0
CA A:LEU18 4.0 13.5 1.0
CG A:ASP19 4.0 19.2 1.0
N A:LEU18 4.1 12.2 1.0
C A:LEU18 4.1 14.4 1.0
C A:ARG122 4.2 12.6 1.0
CA A:ILE123 4.3 14.3 1.0
CA A:ARG122 4.4 14.5 1.0
CB A:GLU17 4.4 15.5 1.0
OD1 A:ASP19 4.5 18.8 1.0
CB A:ARG122 4.5 14.6 1.0
CB A:ASP19 4.5 17.8 1.0
N A:GLU124 4.7 16.5 1.0
CG A:GLU124 4.7 24.6 1.0
CA A:GLU17 4.8 14.7 1.0
CA A:ASP19 4.8 15.9 1.0

Sodium binding site 7 out of 11 in 6quh

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Sodium binding site 7 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na322

b:30.5
occ:0.67
 O A:HOH425 2.6 32.3 1.0
O A:SER175 2.8 19.8 1.0
O A:HOH620 2.8 35.2 1.0
O A:GLY174 3.3 24.5 1.0
CG A:ASN170 3.4 18.8 1.0
CB A:ASN170 3.4 17.0 1.0
O A:HOH421 3.5 38.1 1.0
CA A:ASN170 3.6 16.3 1.0
C A:GLY174 3.6 21.2 1.0
OD1 A:ASN170 3.7 18.9 1.0
C A:SER175 3.7 20.2 1.0
ND2 A:ASN170 3.9 20.0 1.0
N A:VAL171 3.9 17.4 1.0
CG2 A:VAL176 3.9 27.4 1.0
CA A:GLY174 4.2 22.6 1.0
O A:VAL171 4.2 22.6 1.0
C A:ASN170 4.2 15.9 1.0
N A:SER175 4.2 23.9 1.0
O A:HOH634 4.3 36.7 1.0
O A:HOH516 4.3 38.1 1.0
N A:VAL176 4.4 21.6 1.0
CA A:SER175 4.5 20.7 1.0
CA A:VAL176 4.6 19.8 1.0
O A:HOH409 4.6 43.1 1.0
O A:HOH424 4.6 39.1 1.0
CU A:CU306 4.6 32.6 0.3
N A:ASN170 4.8 16.7 1.0
CB A:VAL176 4.9 22.9 1.0

Sodium binding site 8 out of 11 in 6quh

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Sodium binding site 8 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na316

b:20.6
occ:0.91
 O C:THR59 2.7 16.1 1.0
OG1 C:THR62 2.7 13.4 1.0
OG1 C:THR63 2.7 14.4 1.0
N C:THR63 3.0 14.0 1.0
C C:LEU60 3.3 11.3 1.0
CA C:LEU60 3.4 13.9 1.0
CB C:THR63 3.4 15.0 1.0
N C:THR62 3.4 14.0 1.0
O C:LEU60 3.5 14.2 1.0
C C:THR59 3.6 15.4 1.0
CD1 C:ILE98 3.6 16.0 1.0
CL C:CL311 3.7 21.1 0.6
CA C:THR63 3.8 13.9 1.0
C C:THR62 3.8 13.0 1.0
N C:LEU60 3.8 15.6 1.0
N C:VAL61 3.8 14.9 1.0
CA C:THR62 3.9 13.1 1.0
CB C:THR62 3.9 14.2 1.0
CL C:CL308 4.2 20.2 0.5
C C:VAL61 4.3 14.3 1.0
CD2 C:TYR106 4.6 14.7 1.0
NE2 C:HIS181 4.6 12.7 1.0
CL C:CL307 4.7 19.4 0.6
CA C:VAL61 4.7 13.8 1.0
CB C:LEU60 4.7 16.0 1.0
CE2 C:TYR106 4.8 14.5 1.0
CG2 C:THR63 4.8 15.1 1.0
CA C:THR59 4.9 16.7 1.0
CG2 C:THR62 4.9 15.0 1.0
O C:THR62 4.9 15.2 1.0
CD2 C:LEU60 5.0 22.9 1.0

Sodium binding site 9 out of 11 in 6quh

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Sodium binding site 9 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na317

b:24.1
occ:0.96
 OG1 C:THR108 2.7 15.3 1.0
CL C:CL309 2.8 20.6 0.6
O C:GLN94 2.8 16.2 1.0
CB C:THR108 3.5 16.9 1.0
C C:GLN94 3.5 14.5 1.0
CL C:CL307 3.7 19.4 0.6
O C:THR108 3.8 17.2 1.0
C C:THR108 3.8 14.8 1.0
CB C:ALA110 3.8 18.1 1.0
N C:ALA110 3.9 15.8 1.0
CG C:GLN94 3.9 16.6 1.0
CA C:GLU95 4.0 16.0 1.0
N C:ARG109 4.0 15.7 1.0
N C:GLU95 4.0 14.6 1.0
N C:ARG96 4.1 14.9 1.0
C C:ARG109 4.2 16.0 1.0
C C:GLU95 4.2 15.1 1.0
CB C:GLN94 4.2 16.4 1.0
CA C:ARG109 4.2 15.7 1.0
CA C:THR108 4.3 16.8 1.0
NE2 C:GLN94 4.4 15.9 1.0
CG C:ARG96 4.4 13.9 1.0
CL C:CL310 4.5 18.5 0.5
CA C:ALA110 4.5 17.7 1.0
CA C:GLN94 4.5 16.7 1.0
CG2 C:THR108 4.7 16.8 1.0
CD C:GLN94 4.7 14.3 1.0
CB C:ARG96 4.7 15.1 1.0
NH1 C:ARG96 4.8 14.8 1.0
CG2 C:ILE123 4.8 20.3 1.0
CG2 C:THR63 4.9 15.1 1.0
O C:ARG109 5.0 17.6 1.0
CA C:ARG96 5.0 14.1 1.0

Sodium binding site 10 out of 11 in 6quh

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Sodium binding site 10 out of 11 in the Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Ghk Tagged Gfp Variant Crystal Form II at 1.34A Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na318

b:33.5
occ:0.91
 OD1 C:ASP21 2.6 27.8 1.0
O C:GLY127 2.8 17.0 1.0
CG C:ASP21 3.4 32.5 1.0
O C:ASP21 3.5 22.8 1.0
N C:ASN23 3.6 18.6 1.0
N C:GLY24 3.7 16.1 1.0
C C:ASP21 3.9 16.6 1.0
C C:GLY127 3.9 15.5 1.0
CG2 C:THR128 4.0 20.0 1.0
OD2 C:ASP21 4.1 41.6 1.0
CB C:ASP21 4.1 26.6 1.0
CA C:ASN23 4.2 19.9 1.0
N C:GLY127 4.2 17.9 1.0
C C:VAL22 4.3 17.8 1.0
N C:VAL22 4.3 17.1 1.0
CA C:VAL22 4.4 17.3 1.0
C C:ASN23 4.4 16.4 1.0
CA C:GLY24 4.5 19.2 1.0
CA C:ASP21 4.6 22.1 1.0
CA C:GLY127 4.8 18.0 1.0
N C:THR128 4.8 16.9 1.0
C C:ARG126 4.8 17.5 1.0
CA C:THR128 4.8 15.4 1.0
CA C:ARG126 4.9 15.9 1.0
CB C:ARG126 4.9 20.5 1.0

Reference:

T.Huyton, D.Goerlich. Using the Copper Binding Peptide Ghk For Phasing Structures To Be Published.
Page generated: Tue Oct 8 12:58:58 2024

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