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Sodium in PDB 6yg1: Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix

Enzymatic activity of Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix

All present enzymatic activity of Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix:
2.7.12.2;

Protein crystallography data

The structure of Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix, PDB code: 6yg1 was solved by A.Chaikuad, S.Knapp, Structural Genomics Consortium (Sgc), Scottishstructural Proteomics Facility (Sspf), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.83 / 2.22
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.160, 67.870, 142.780, 90.00, 114.76, 90.00
R / Rfree (%) 20.4 / 23.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix (pdb code 6yg1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix, PDB code: 6yg1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6yg1

Go back to Sodium Binding Sites List in 6yg1
Sodium binding site 1 out of 4 in the Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix


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 MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:19.1
occ:1.00
 OE1 A:GLN197 2.4 47.6 1.0
O A:CYS192 2.5 36.8 1.0
O A:ILE195 2.6 36.2 1.0
O A:HOH647 2.7 32.5 1.0
O A:HIS190 2.9 38.3 1.0
O A:SER189 2.9 37.1 1.0
CD A:GLN197 3.4 48.0 1.0
C A:HIS190 3.4 40.9 1.0
C A:CYS192 3.6 37.6 1.0
C A:ILE195 3.7 34.1 1.0
NE2 A:GLN197 3.8 52.5 1.0
CA A:HIS190 3.8 42.0 1.0
C A:SER189 3.8 37.9 1.0
O A:VAL196 4.0 39.1 1.0
N A:CYS192 4.1 38.7 1.0
CB A:ILE195 4.2 33.1 1.0
N A:HIS190 4.2 39.5 1.0
C A:VAL196 4.3 37.4 1.0
CA A:ILE195 4.3 33.1 1.0
CA A:CYS192 4.3 38.1 1.0
N A:ILE195 4.4 32.9 1.0
N A:ASP191 4.4 41.6 1.0
CG2 A:ILE195 4.6 33.5 1.0
CA A:GLN197 4.6 39.5 1.0
N A:PRO193 4.6 37.4 1.0
CG A:GLN197 4.6 47.9 1.0
N A:GLN197 4.7 38.5 1.0
N A:VAL196 4.7 33.6 1.0
C A:ASP191 4.7 40.7 1.0
CB A:CYS192 4.7 38.6 1.0
CA A:PRO193 4.7 37.2 1.0
CB A:GLN197 4.9 42.6 1.0
O A:HOH684 4.9 43.8 1.0
CB A:SER189 5.0 38.5 1.0
CA A:VAL196 5.0 34.7 1.0

Sodium binding site 2 out of 4 in 6yg1

Go back to Sodium Binding Sites List in 6yg1
Sodium binding site 2 out of 4 in the Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix


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 MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:51.4
occ:1.00
 OE1 B:GLN197 2.4 74.5 1.0
O B:CYS192 2.5 64.9 1.0
O B:SER189 2.5 67.9 1.0
O B:ILE195 2.8 60.6 1.0
O B:HIS190 3.1 72.9 1.0
CD B:GLN197 3.4 77.2 1.0
C B:HIS190 3.5 74.1 1.0
C B:CYS192 3.5 64.7 1.0
C B:SER189 3.6 70.8 1.0
CA B:HIS190 3.8 75.9 1.0
C B:ILE195 3.8 58.7 1.0
N B:CYS192 3.9 69.9 1.0
NE2 B:GLN197 3.9 80.0 1.0
N B:HIS190 4.1 74.0 1.0
O B:VAL196 4.1 67.4 1.0
CB B:ILE195 4.1 57.4 1.0
CA B:CYS192 4.2 66.3 1.0
N B:ASP191 4.4 73.4 1.0
CA B:ILE195 4.4 57.0 1.0
CB B:CYS192 4.5 65.3 1.0
N B:ILE195 4.5 56.1 1.0
CG2 B:ILE195 4.5 58.1 1.0
C B:VAL196 4.5 64.8 1.0
CB B:SER189 4.6 67.7 1.0
N B:PRO193 4.6 63.4 1.0
CA B:GLN197 4.7 68.5 1.0
C B:ASP191 4.7 71.2 1.0
CG B:GLN197 4.7 75.8 1.0
CA B:SER189 4.7 71.1 1.0
CA B:PRO193 4.9 61.6 1.0
N B:GLN197 4.9 65.8 1.0
N B:VAL196 4.9 58.5 1.0
CB B:GLN197 4.9 71.0 1.0

Sodium binding site 3 out of 4 in 6yg1

Go back to Sodium Binding Sites List in 6yg1
Sodium binding site 3 out of 4 in the Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix


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 MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:48.6
occ:1.00
 OE1 C:GLN197 2.3 71.4 1.0
O C:ILE195 2.6 49.3 1.0
O C:CYS192 2.6 55.2 1.0
O C:SER189 2.7 65.0 1.0
O C:HIS190 3.3 77.2 1.0
CD C:GLN197 3.4 71.4 1.0
C C:ILE195 3.6 49.5 1.0
C C:SER189 3.7 68.2 1.0
C C:HIS190 3.7 77.1 1.0
C C:CYS192 3.8 58.1 1.0
O C:VAL196 3.8 56.6 1.0
CA C:HIS190 3.9 77.9 1.0
NE2 C:GLN197 4.0 75.6 1.0
CB C:ILE195 4.1 48.5 1.0
N C:CYS192 4.1 64.1 1.0
C C:VAL196 4.2 55.5 1.0
N C:HIS190 4.2 73.0 1.0
CA C:ILE195 4.3 48.4 1.0
CA C:GLN197 4.4 61.0 1.0
CG2 C:ILE195 4.4 48.2 1.0
CA C:CYS192 4.4 60.1 1.0
O C:HOH632 4.5 62.3 1.0
N C:ILE195 4.5 48.2 1.0
N C:GLN197 4.5 58.2 1.0
CG C:GLN197 4.5 69.0 1.0
N C:ASP191 4.6 77.0 1.0
CB C:GLN197 4.6 64.4 1.0
N C:VAL196 4.6 51.4 1.0
CB C:CYS192 4.7 58.4 1.0
CB C:SER189 4.7 63.3 1.0
N C:PRO193 4.8 57.9 1.0
CA C:SER189 4.9 67.1 1.0
CA C:VAL196 4.9 53.3 1.0
C C:ASP191 4.9 69.7 1.0
CA C:PRO193 5.0 56.8 1.0

Sodium binding site 4 out of 4 in 6yg1

Go back to Sodium Binding Sites List in 6yg1
Sodium binding site 4 out of 4 in the Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:40.0
occ:0.50
 O C:THR417 2.4 51.9 1.0
O C:MET414 2.5 47.6 1.0
O C:ALA415 3.1 50.8 1.0
C C:ALA415 3.6 50.5 1.0
C C:THR417 3.6 54.2 1.0
C C:MET414 3.7 47.2 1.0
NH1 C:ARG225 3.8 54.8 1.0
CA C:ALA415 3.9 49.5 1.0
N C:THR417 4.0 53.8 1.0
N C:ALA415 4.3 47.6 1.0
N C:LYS416 4.4 51.5 1.0
CA C:THR417 4.5 53.3 1.0
N C:GLU418 4.5 56.8 1.0
CA C:GLU418 4.5 58.9 1.0
C C:LYS416 4.5 55.5 1.0
CA C:MET414 4.8 46.7 1.0
CA C:LYS416 4.9 55.5 1.0

Reference:

M.Schroder, L.Tan, J.Wang, Y.Liang, N.S.Gray, S.Knapp, A.Chaikuad. Catalytic Domain Plasticity of MKK7 Reveals Structural Mechanisms of Allosteric Activation and Diverse Targeting Opportunities. Cell Chem Biol V. 27 1285 2020.
ISSN: ESSN 2451-9456
PubMed: 32783966
DOI: 10.1016/J.CHEMBIOL.2020.07.014
Page generated: Tue Oct 8 15:07:43 2024

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