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Sodium in PDB 9rwd: High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine)

Enzymatic activity of High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine)

All present enzymatic activity of High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine):
2.1.2.1;

Protein crystallography data

The structure of High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine), PDB code: 9rwd was solved by A.Warlich, M.Ruszkowski, D.Nawrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.06 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.184, 125.571, 135.137, 90, 93.68, 90
R / Rfree (%) 14.5 / 17.8

Sodium Binding Sites:

The binding sites of Sodium atom in the High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine) (pdb code 9rwd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine), PDB code: 9rwd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 9rwd

Go back to Sodium Binding Sites List in 9rwd
Sodium binding site 1 out of 4 in the High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:37.0
occ:1.00
 O A:HOH1112 2.3 52.2 1.0
O A:LYS459 2.3 26.7 1.0
O A:THR462 2.4 32.3 1.0
O A:HOH1130 2.4 50.3 1.0
O A:HOH902 2.5 27.7 1.0
C A:LYS459 3.5 26.2 1.0
C A:THR462 3.6 31.3 1.0
CG A:LYS459 4.1 27.1 1.0
O A:HOH793 4.2 24.7 1.0
N A:THR462 4.2 29.7 1.0
CA A:SER460 4.3 28.5 1.0
O A:HOH1125 4.3 44.1 1.0
N A:SER460 4.3 26.8 1.0
C A:SER460 4.4 29.9 1.0
CA A:LYS459 4.4 24.9 1.0
CA A:ALA463 4.4 32.4 1.0
N A:ALA463 4.5 32.8 1.0
CA A:THR462 4.6 29.1 1.0
O A:ALA463 4.6 32.8 1.0
O A:SER460 4.7 31.5 1.0
N A:LYS461 4.8 29.6 1.0
CB A:LYS459 4.9 25.6 1.0
OG1 A:THR462 5.0 26.2 1.0

Sodium binding site 2 out of 4 in 9rwd

Go back to Sodium Binding Sites List in 9rwd
Sodium binding site 2 out of 4 in the High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na606

b:26.8
occ:1.00
 O B:HOH1096 2.2 46.2 1.0
O B:THR462 2.3 26.3 1.0
O B:HOH787 2.5 27.6 1.0
O B:LYS459 2.5 24.1 1.0
O B:HOH1142 2.6 49.3 1.0
O B:HOH1057 2.7 41.4 1.0
C B:THR462 3.6 25.5 1.0
C B:LYS459 3.6 23.3 1.0
CG B:LYS459 4.1 23.1 1.0
O B:HOH789 4.2 22.0 1.0
N B:THR462 4.3 26.0 1.0
CA B:ALA463 4.3 26.8 1.0
N B:ALA463 4.4 26.1 1.0
O B:ALA463 4.4 27.6 1.0
CA B:LYS459 4.5 22.3 1.0
N B:SER460 4.5 24.6 1.0
CA B:SER460 4.5 26.3 1.0
CA B:THR462 4.6 24.8 1.0
C B:SER460 4.6 27.4 1.0
O B:HOH1148 4.6 39.6 1.0
O B:SER460 4.9 29.8 1.0
C B:ALA463 4.9 27.4 1.0
CB B:LYS459 4.9 22.6 1.0
N B:LYS461 5.0 27.4 1.0

Sodium binding site 3 out of 4 in 9rwd

Go back to Sodium Binding Sites List in 9rwd
Sodium binding site 3 out of 4 in the High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na606

b:30.8
occ:1.00
 O C:THR462 2.3 27.1 1.0
O C:HOH1044 2.4 52.3 1.0
O C:HOH1048 2.4 40.3 1.0
O C:LYS459 2.5 25.9 1.0
O C:HOH843 2.5 31.9 1.0
C C:THR462 3.5 26.1 1.0
C C:LYS459 3.7 26.4 1.0
O C:HOH836 4.2 21.1 1.0
CG C:LYS459 4.2 27.6 1.0
N C:THR462 4.2 27.5 1.0
CA C:ALA463 4.3 25.6 1.0
N C:ALA463 4.4 25.8 1.0
O C:ALA463 4.5 24.8 1.0
CA C:SER460 4.5 28.7 1.0
C C:SER460 4.5 30.2 1.0
CA C:THR462 4.5 26.5 1.0
N C:SER460 4.6 27.1 1.0
CA C:LYS459 4.6 25.8 1.0
O C:HOH1099 4.7 38.0 1.0
O C:SER460 4.7 31.8 1.0
O C:HOH1108 4.8 38.9 1.0
N C:LYS461 4.9 29.5 1.0
C C:ALA463 4.9 24.5 1.0

Sodium binding site 4 out of 4 in 9rwd

Go back to Sodium Binding Sites List in 9rwd
Sodium binding site 4 out of 4 in the High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na605

b:47.9
occ:1.00
 O D:THR462 2.4 35.6 1.0
O D:HOH1065 2.5 50.5 1.0
O D:HOH722 2.7 32.5 1.0
O D:LYS459 2.7 33.3 1.0
C D:THR462 3.6 35.3 1.0
C D:LYS459 3.9 33.0 1.0
CA D:ALA463 4.3 35.1 1.0
CG D:LYS459 4.3 34.1 1.0
O D:HOH783 4.4 26.2 1.0
N D:ALA463 4.4 35.0 1.0
N D:THR462 4.5 34.6 1.0
O D:HOH1053 4.5 43.2 1.0
O D:ALA463 4.6 36.3 1.0
CA D:SER460 4.6 34.8 1.0
N D:SER460 4.7 34.1 1.0
CA D:THR462 4.7 34.4 1.0
C D:SER460 4.7 35.5 1.0
CA D:LYS459 4.8 32.3 1.0
C D:ALA463 4.9 36.1 1.0
O D:SER460 4.9 35.5 1.0

Reference:

A.Warlich, M.Ruszkowski, D.Nawrot. High-Resolution Structure of Human SHMT2 with Covalently Bound Plp (Internal Aldimine) To Be Published.
Page generated: Mon Aug 18 17:34:34 2025

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