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Gadolinium in PDB 3akc: Crystal Structure of Cmp Kinase in Complex with Cdp and Adp From Thermus Thermophilus HB8

Enzymatic activity of Crystal Structure of Cmp Kinase in Complex with Cdp and Adp From Thermus Thermophilus HB8

All present enzymatic activity of Crystal Structure of Cmp Kinase in Complex with Cdp and Adp From Thermus Thermophilus HB8:
2.7.4.14;

Protein crystallography data

The structure of Crystal Structure of Cmp Kinase in Complex with Cdp and Adp From Thermus Thermophilus HB8, PDB code: 3akc was solved by R.Mega, N.Nakagawa, S.Kuramitsu, R.Masui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.65 / 1.65
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 62.206, 62.206, 110.951, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 22

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Crystal Structure of Cmp Kinase in Complex with Cdp and Adp From Thermus Thermophilus HB8 (pdb code 3akc). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total only one binding site of Gadolinium was determined in the Crystal Structure of Cmp Kinase in Complex with Cdp and Adp From Thermus Thermophilus HB8, PDB code: 3akc:

Gadolinium binding site 1 out of 1 in 3akc

Go back to Gadolinium Binding Sites List in 3akc
Gadolinium binding site 1 out of 1 in the Crystal Structure of Cmp Kinase in Complex with Cdp and Adp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Crystal Structure of Cmp Kinase in Complex with Cdp and Adp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd211

b:15.6
occ:1.00
 O2B A:CDP209 2.4 28.2 1.0
OG A:SER16 2.4 10.7 1.0
O A:HOH269 2.4 20.3 1.0
O A:HOH223 2.4 20.4 1.0
O3B A:ADP210 2.4 27.9 1.0
O A:HOH218 2.5 10.7 1.0
O A:HOH226 2.5 21.5 1.0
O2A A:ADP210 2.6 28.1 1.0
O2B A:ADP210 3.0 28.4 1.0
PB A:ADP210 3.2 26.8 1.0
CB A:SER16 3.5 12.4 1.0
PB A:CDP209 3.7 28.2 1.0
PA A:ADP210 3.8 27.3 1.0
O3A A:ADP210 3.9 28.2 1.0
O1B A:CDP209 4.2 28.5 1.0
N A:SER16 4.3 12.6 1.0
O A:HOH283 4.4 32.7 1.0
NH2 A:ARG153 4.4 17.7 1.0
O1A A:CDP209 4.4 27.8 1.0
O3B A:CDP209 4.4 28.3 1.0
O2A A:CDP209 4.4 28.5 1.0
O A:HOH313 4.4 38.8 1.0
O1B A:ADP210 4.5 27.9 1.0
CA A:SER16 4.5 13.4 1.0
O1A A:ADP210 4.6 28.7 1.0
O3A A:CDP209 4.7 28.3 1.0
O5' A:ADP210 4.7 28.7 1.0
PA A:CDP209 4.7 26.2 1.0
OE2 A:GLU124 4.7 13.0 1.0
CE1 A:HIS89 4.9 24.4 1.0
OE1 A:GLU124 4.9 13.6 1.0

Reference:

R.Mega, N.Nakagawa, S.Kuramitsu, R.Masui. The Crystal Structure of the Tertiary Complex of Cmp Kinase with A Phosphoryl Group Acceptor and A Donor From Thermus Thermophilus HB8 To Be Published.
Page generated: Fri Aug 8 08:27:07 2025

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