Sodium in PDB 6uj7: Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide

All present enzymatic activity of Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide:
1.1.1.42;

The structure of Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide, PDB code: 6uj7 was solved by M.S.Miller, P.Thirawatananond, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.43 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.038, 70.67, 87.482, 90, 107.39, 90
R / Rfree (%)	18.2 / 23.8

The structure of Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide (pdb code 6uj7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide, PDB code: 6uj7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:42.3 occ:1.00 O A:HOH536 2.3 35.8 1.0 O A:GLU55 2.4 24.8 1.0 O A:HOH549 2.4 40.5 1.0 O A:HOH548 2.5 43.4 1.0 O A:GLU53 2.6 29.8 1.0 C A:GLU55 3.5 28.0 1.0 C A:GLU53 3.7 28.7 1.0 O A:HOH530 3.7 42.6 1.0 NE1 A:TRP60 3.9 29.7 1.0 CA A:GLU53 4.2 30.2 1.0 O A:HOH574 4.3 46.0 1.0 CA A:GLY56 4.3 32.3 1.0 N A:GLY56 4.3 29.9 1.0 N A:GLU55 4.4 26.4 1.0 C A:GLN54 4.5 29.9 1.0 O A:HOH537 4.6 33.6 1.0 CA A:GLU55 4.6 25.7 1.0 O A:GLN54 4.6 28.3 1.0 CD1 A:TRP60 4.7 32.0 1.0 CB A:GLU53 4.7 35.8 1.0 N A:GLN54 4.7 27.3 1.0 C A:GLY56 4.7 33.5 1.0 CE2 A:TRP60 4.8 25.9 1.0 CA A:GLN54 5.0 32.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:46.9 occ:1.00 O B:HOH346 2.2 47.7 1.0 O B:HOH345 2.3 45.0 1.0 O B:LEU107 2.3 38.3 1.0 O B:HOH307 2.4 46.5 1.0 O B:HIS104 2.7 32.1 1.0 OD1 B:ASN103 2.7 39.5 1.0 C B:HIS104 3.5 32.9 1.0 CG B:ASN103 3.6 40.5 1.0 C B:LEU107 3.6 37.0 1.0 ND2 B:ASN103 3.9 41.6 1.0 N B:HIS104 4.0 32.0 1.0 O B:SER108 4.2 52.8 1.0 N B:VAL105 4.2 34.5 1.0 CA B:VAL105 4.2 35.6 1.0 O B:VAL105 4.3 35.4 1.0 C B:VAL105 4.3 35.4 1.0 N B:LEU107 4.4 34.1 1.0 CA B:LEU107 4.4 38.5 1.0 CA B:HIS104 4.4 31.3 1.0 C B:SER108 4.5 50.3 1.0 CB B:LEU107 4.5 38.5 1.0 N B:SER108 4.6 44.1 1.0 CA B:SER108 4.7 45.0 1.0 CB B:ASN103 4.9 34.5 1.0 C B:ASN103 5.0 32.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:39.0 occ:1.00 O D:HOH513 2.1 32.1 1.0 O D:HOH476 2.2 48.2 1.0 O D:THR187 2.3 29.7 1.0 O A:HOH541 2.4 49.2 1.0 O A:HOH530 2.5 42.6 1.0 O A:GLN54 2.6 28.3 1.0 N D:THR187 3.4 26.3 1.0 C D:THR187 3.4 26.7 1.0 C A:GLN54 3.6 29.9 1.0 OG1 D:THR187 3.7 30.4 1.0 CA D:THR187 3.9 26.0 1.0 O D:HOH560 3.9 39.9 1.0 CA A:GLN54 3.9 32.5 1.0 C D:LYS186 4.4 26.9 1.0 CB A:GLN54 4.4 39.8 1.0 CB D:THR187 4.4 27.2 1.0 N D:HIS188 4.6 25.4 1.0 CA D:LYS186 4.7 30.4 1.0 N A:GLU55 4.8 26.4 1.0 O A:GLU53 4.9 29.8 1.0 CA D:HIS188 5.0 27.2 1.0

M.S.Hwang, M.S.Miller, J.Douglass, P.Thirawatananond, T.Aytenfisu, K.Wright, A.Skora, M.Murphy, K.W.Kinzler, B.Vogelstein, S.Zhou, S.B.Gabelli. Crystal Structure of Hla-B*07:02 with R140Q Mutant IDH2 Peptide To Be Published.