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Sodium in PDB 7ala: Human Gch-Gfrp Inhibitory Complex

Enzymatic activity of Human Gch-Gfrp Inhibitory Complex

All present enzymatic activity of Human Gch-Gfrp Inhibitory Complex:
3.5.4.16;

Protein crystallography data

The structure of Human Gch-Gfrp Inhibitory Complex, PDB code: 7ala was solved by R.Ebenhoch, H.Nar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.74 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.745, 114.013, 113.83, 90, 130.34, 90
R / Rfree (%) 18.5 / 22

Other elements in 7ala:

The structure of Human Gch-Gfrp Inhibitory Complex also contains other interesting chemical elements:

Fluorine (F) 5 atoms
Zinc (Zn) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Gch-Gfrp Inhibitory Complex (pdb code 7ala). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Human Gch-Gfrp Inhibitory Complex, PDB code: 7ala:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7ala

Go back to Sodium Binding Sites List in 7ala
Sodium binding site 1 out of 5 in the Human Gch-Gfrp Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Gch-Gfrp Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na101

b:21.5
occ:1.00
O F:VAL14 2.2 23.4 1.0
O F:GLN9 2.3 15.8 1.0
O F:ARG11 2.3 21.1 1.0
OG1 F:THR8 2.5 20.1 1.0
C F:ARG11 3.4 20.4 1.0
C F:VAL14 3.4 23.7 1.0
CG2 F:THR8 3.5 17.0 1.0
C F:GLN9 3.5 17.0 1.0
CB F:THR8 3.6 17.8 1.0
O F:HOH238 3.7 26.0 1.0
N F:GLN9 3.9 15.8 1.0
CG1 F:VAL14 3.9 25.4 1.0
CA F:MET12 4.2 21.4 1.0
N F:MET12 4.2 20.6 1.0
N F:VAL14 4.2 23.0 1.0
O F:GLY15 4.2 21.5 1.0
N F:ARG11 4.2 19.7 1.0
CA F:VAL14 4.3 23.8 1.0
N F:GLY15 4.3 23.0 1.0
CA F:GLN9 4.3 16.3 1.0
CA F:ARG11 4.4 19.2 1.0
C F:THR8 4.4 15.7 1.0
CA F:GLY15 4.4 22.1 1.0
C F:GLY15 4.4 21.3 1.0
O F:PRO16 4.4 22.2 1.0
C F:ILE10 4.4 20.4 1.0
C F:MET12 4.4 22.3 1.0
O F:HOH235 4.5 28.3 1.0
CA F:THR8 4.5 15.4 1.0
N F:ILE10 4.5 18.5 1.0
CA F:ILE10 4.5 19.9 1.0
O F:MET12 4.7 22.4 1.0
CB F:VAL14 4.8 25.7 1.0
O F:ILE10 4.8 21.4 1.0
CB F:GLN9 4.9 17.8 1.0

Sodium binding site 2 out of 5 in 7ala

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Sodium binding site 2 out of 5 in the Human Gch-Gfrp Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Gch-Gfrp Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na101

b:22.3
occ:1.00
O G:GLN9 2.3 21.9 1.0
O G:ARG11 2.3 20.4 1.0
O G:VAL14 2.4 19.2 1.0
O G:HOH252 2.4 17.2 1.0
OG1 G:THR8 2.5 19.4 1.0
C G:ARG11 3.4 19.8 1.0
CG2 G:THR8 3.5 17.0 1.0
C G:GLN9 3.5 20.6 1.0
CB G:THR8 3.5 18.4 1.0
C G:VAL14 3.5 19.1 1.0
N G:GLN9 3.7 19.2 1.0
O G:HOH225 4.0 22.0 1.0
N G:ARG11 4.1 19.0 1.0
CG1 G:VAL14 4.1 19.9 1.0
N G:MET12 4.1 19.1 1.0
CA G:MET12 4.1 19.7 1.0
CA G:GLN9 4.2 19.8 1.0
C G:THR8 4.2 18.4 1.0
O G:GLY15 4.3 19.8 1.0
CA G:ARG11 4.3 18.5 1.0
C G:ILE10 4.3 19.5 1.0
N G:VAL14 4.4 18.4 1.0
CA G:THR8 4.4 18.5 1.0
O G:HOH223 4.4 27.0 1.0
O G:PRO16 4.4 18.8 1.0
N G:GLY15 4.4 19.0 1.0
CA G:VAL14 4.5 18.8 1.0
C G:GLY15 4.5 19.5 1.0
C G:MET12 4.5 19.8 1.0
N G:ILE10 4.5 20.0 1.0
CA G:GLY15 4.5 19.2 1.0
CA G:ILE10 4.7 20.3 1.0
O G:ILE10 4.7 19.0 1.0
CB G:GLN9 4.8 22.4 1.0
O G:MET12 4.8 19.6 1.0
CB G:VAL14 4.9 19.3 1.0

Sodium binding site 3 out of 5 in 7ala

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Sodium binding site 3 out of 5 in the Human Gch-Gfrp Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Gch-Gfrp Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na101

b:29.8
occ:1.00
O H:GLN9 2.2 21.6 1.0
O H:ARG11 2.3 19.8 1.0
O H:VAL14 2.4 20.6 1.0
OG1 H:THR8 2.5 21.4 1.0
C H:ARG11 3.4 19.3 1.0
C H:GLN9 3.4 20.9 1.0
CG2 H:THR8 3.5 19.9 1.0
CB H:THR8 3.6 20.2 1.0
C H:VAL14 3.6 21.6 1.0
N H:GLN9 3.7 20.0 1.0
O H:HOH224 3.7 24.5 1.0
N H:ARG11 4.1 19.9 1.0
CG1 H:VAL14 4.1 23.3 1.0
CA H:GLN9 4.1 20.6 1.0
N H:MET12 4.2 18.7 1.0
CA H:MET12 4.2 18.6 1.0
C H:THR8 4.2 19.7 1.0
C H:ILE10 4.3 21.2 1.0
CA H:ARG11 4.3 19.2 1.0
O H:HOH209 4.3 26.3 1.0
O H:GLY15 4.4 22.8 1.0
CA H:THR8 4.4 19.4 1.0
N H:VAL14 4.4 20.9 1.0
O H:PRO16 4.4 24.5 1.0
N H:ILE10 4.4 20.8 1.0
CA H:VAL14 4.5 21.7 1.0
N H:GLY15 4.5 22.1 1.0
C H:GLY15 4.5 22.4 1.0
CA H:GLY15 4.5 22.2 1.0
C H:MET12 4.5 19.0 1.0
O H:ILE10 4.6 21.5 1.0
CA H:ILE10 4.6 20.9 1.0
CB H:GLN9 4.7 22.0 1.0
O H:MET12 4.9 18.6 1.0
CB H:VAL14 4.9 23.2 1.0

Sodium binding site 4 out of 5 in 7ala

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Sodium binding site 4 out of 5 in the Human Gch-Gfrp Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Gch-Gfrp Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na101

b:25.1
occ:1.00
O I:ARG11 2.2 21.9 1.0
O I:VAL14 2.2 20.6 1.0
O I:GLN9 2.3 20.4 1.0
OG1 I:THR8 2.6 23.6 1.0
C I:ARG11 3.3 21.6 1.0
C I:VAL14 3.4 21.7 1.0
C I:GLN9 3.6 21.0 1.0
CG2 I:THR8 3.6 22.5 1.0
CB I:THR8 3.7 22.5 1.0
O I:HOH222 3.7 20.4 1.0
N I:GLN9 3.9 20.4 1.0
CG1 I:VAL14 4.0 24.3 1.0
N I:ARG11 4.1 21.2 1.0
N I:MET12 4.1 21.0 1.0
CA I:MET12 4.1 21.7 1.0
N I:VAL14 4.2 22.5 1.0
O I:GLY15 4.3 23.1 1.0
CA I:ARG11 4.3 21.3 1.0
CA I:VAL14 4.3 22.5 1.0
N I:GLY15 4.3 22.1 1.0
CA I:GLN9 4.3 20.9 1.0
C I:ILE10 4.4 22.6 1.0
C I:THR8 4.4 20.4 1.0
CA I:GLY15 4.4 22.6 1.0
C I:MET12 4.4 22.6 1.0
C I:GLY15 4.4 22.7 1.0
O I:PRO16 4.5 24.6 1.0
N I:ILE10 4.5 21.7 1.0
CA I:THR8 4.5 21.1 1.0
CA I:ILE10 4.6 23.1 1.0
F19 B:5RW302 4.7 56.7 1.0
O I:MET12 4.7 23.3 1.0
O I:ILE10 4.8 24.4 1.0
CB I:VAL14 4.8 23.8 1.0
CB I:GLN9 4.9 22.4 1.0
N I:GLU13 5.0 22.4 1.0

Sodium binding site 5 out of 5 in 7ala

Go back to Sodium Binding Sites List in 7ala
Sodium binding site 5 out of 5 in the Human Gch-Gfrp Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Gch-Gfrp Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na101

b:21.8
occ:1.00
O J:VAL14 2.3 22.1 1.0
O J:ARG11 2.3 19.2 1.0
O J:GLN9 2.4 23.1 1.0
O J:HOH247 2.4 19.2 1.0
OG1 J:THR8 2.6 23.4 1.0
C J:ARG11 3.4 19.5 1.0
C J:VAL14 3.4 22.8 1.0
CG2 J:THR8 3.5 21.6 1.0
C J:GLN9 3.6 23.0 1.0
CB J:THR8 3.6 21.7 1.0
O J:HOH242 3.6 25.0 1.0
N J:GLN9 3.8 21.7 1.0
CG1 J:VAL14 4.0 23.9 1.0
N J:ARG11 4.2 21.7 1.0
O J:GLY15 4.2 22.7 1.0
CA J:MET12 4.2 20.4 1.0
N J:MET12 4.2 19.1 1.0
CA J:GLN9 4.3 22.2 1.0
N J:VAL14 4.3 22.8 1.0
C J:THR8 4.3 21.2 1.0
N J:GLY15 4.3 22.8 1.0
CA J:VAL14 4.4 23.1 1.0
C J:GLY15 4.4 22.5 1.0
O J:PRO16 4.4 21.8 1.0
CA J:GLY15 4.4 22.8 1.0
CA J:ARG11 4.4 20.0 1.0
C J:ILE10 4.4 22.9 1.0
CA J:THR8 4.4 20.3 1.0
C J:MET12 4.5 21.7 1.0
N J:ILE10 4.6 23.4 1.0
O J:HOH211 4.6 31.4 1.0
CB J:GLN9 4.8 22.7 1.0
O J:MET12 4.8 21.8 1.0
O J:ILE10 4.8 22.9 1.0
CA J:ILE10 4.8 24.1 1.0
CB J:VAL14 4.8 24.2 1.0

Reference:

R.Ebenhoch, M.Bauer, D.Reinert, A.Kersting, S.Huber, A.Schmid, I.Hinz, M.Feiler, K.Mueller, H.Nar. Using Hybrid Approaches to Study the Allosteric Regulation of Gtp Cyclohydrolase I To Be Published.
Page generated: Fri Nov 5 16:01:50 2021

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