Sodium in PDB 5m85: Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803

The structure of Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803, PDB code: 5m85 was solved by X.-L.Xu, K.-H.Zhao, W.Gaertner, A.Hoeppner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.04 / 2.10
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	75.101, 75.101, 71.210, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 22.2

The binding sites of Sodium atom in the Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803 (pdb code 5m85). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803, PDB code: 5m85:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:44.3 occ:1.00 OH A:TYR509 2.6 26.0 1.0 O2D A:CYC701 2.6 31.2 1.0 O2A A:CYC701 2.8 25.9 1.0 CE2 A:TYR509 3.2 28.5 1.0 CZ A:TYR509 3.3 28.8 1.0 CGD A:CYC701 3.3 31.4 1.0 CBA A:CYC701 3.3 27.9 1.0 CGA A:CYC701 3.4 30.2 1.0 CBD A:CYC701 3.5 29.6 1.0 CAA A:CYC701 3.5 28.6 1.0 CAD A:CYC701 3.6 29.6 1.0 CD2 A:LEU515 3.7 38.7 1.0 CHA A:CYC701 4.0 28.6 1.0 NE A:ARG508 4.3 31.1 1.0 O A:HOH836 4.4 31.1 1.0 O1D A:CYC701 4.4 30.8 1.0 C2A A:CYC701 4.5 28.7 1.0 CG A:LEU515 4.5 37.0 1.0 CD2 A:TYR509 4.5 30.1 1.0 CB A:LEU515 4.5 33.8 1.0 CE1 A:TYR509 4.6 28.4 1.0 CD A:ARG508 4.6 28.9 1.0 C3D A:CYC701 4.6 29.1 1.0 O1A A:CYC701 4.6 28.7 1.0 CD1 A:LEU515 4.6 42.6 1.0 CG A:ARG508 4.6 29.9 1.0 C1A A:CYC701 4.7 30.9 1.0 CD2 A:LEU501 4.7 32.9 1.0 C4D A:CYC701 4.8 31.6 1.0

Sodium binding site 2 out of 4 in the Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:52.5 occ:1.00 NE2 A:GLN588 3.2 41.2 1.0 CE2 A:TYR587 3.5 49.2 1.0 CD2 A:TYR587 3.6 49.8 1.0 CG A:GLN588 3.7 40.2 1.0 CD1 A:LEU591 3.7 49.2 1.0 CD A:GLN588 4.0 42.4 1.0 CZ A:TYR587 4.8 51.6 1.0 CG A:TYR587 5.0 44.6 1.0

Sodium binding site 3 out of 4 in the Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:31.0 occ:1.00 O A:HOH862 2.8 32.5 1.0 OG1 A:THR526 3.0 35.4 1.0 ND1 A:HIS529 3.0 30.6 1.0 N A:THR526 3.1 29.5 1.0 CB A:HIS529 3.5 31.9 1.0 CMD A:CYC701 3.5 28.1 1.0 CD1 A:PHE525 3.7 28.3 1.0 CG A:HIS529 3.7 33.0 1.0 CB A:THR526 3.7 31.5 1.0 C2D A:CYC701 3.7 25.6 1.0 CA A:PHE525 3.7 31.7 1.0 CG2 A:THR526 3.8 35.9 1.0 CB A:PHE525 3.8 31.3 1.0 CHD A:CYC701 3.9 26.7 1.0 C A:PHE525 3.9 27.5 1.0 C1D A:CYC701 3.9 31.0 1.0 CA A:THR526 4.0 29.6 1.0 CAI A:3CX702 4.1 32.0 1.0 O A:HOH851 4.1 38.0 1.0 CE1 A:HIS529 4.2 29.7 1.0 CG A:PHE525 4.2 26.3 1.0 O A:HOH868 4.6 34.7 1.0 C3D A:CYC701 4.7 29.1 1.0 CE1 A:PHE525 4.7 32.5 1.0 NAL A:3CX702 4.7 32.3 1.0 O A:THR526 4.7 31.7 1.0 CBD A:CYC701 4.8 29.6 1.0 C A:THR526 4.8 34.5 1.0 ND A:CYC701 4.9 31.3 1.0 CAN A:3CX702 4.9 34.9 1.0 CD2 A:HIS529 5.0 31.4 1.0 CA A:HIS529 5.0 29.9 1.0 O A:HOH871 5.0 41.6 1.0 CAG A:3CX702 5.0 34.9 1.0

Sodium binding site 4 out of 4 in the Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Three-Dimensional Structure of the Intermediate State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:41.1 occ:1.00 OD1 A:ASP498 2.7 28.5 1.0 O A:HOH861 2.8 29.9 1.0 O A:HOH860 2.9 28.7 1.0 N A:LEU501 3.1 36.5 1.0 N A:TYR500 3.4 31.6 1.0 O A:ASP498 3.5 33.8 1.0 CG A:ASP498 3.5 30.0 1.0 CB A:LEU501 3.7 32.6 1.0 CG A:LEU501 3.7 32.5 1.0 O A:HOH841 3.7 31.9 1.0 C A:ASP498 3.7 32.2 1.0 NA A:CYC701 3.8 28.2 1.0 CA A:TYR500 3.9 32.2 1.0 CB A:TYR500 4.0 34.8 1.0 C A:THR499 4.0 29.7 1.0 CA A:LEU501 4.0 31.8 1.0 C1A A:CYC701 4.0 30.9 1.0 C A:TYR500 4.0 34.4 1.0 C4A A:CYC701 4.0 31.3 1.0 CD1 A:LEU501 4.1 35.3 1.0 N A:THR499 4.2 31.4 1.0 CB A:ASP498 4.2 29.8 1.0 CA A:THR499 4.2 33.5 1.0 OD2 A:ASP498 4.3 27.6 1.0 CHA A:CYC701 4.4 28.6 1.0 C2A A:CYC701 4.5 28.7 1.0 CA A:ASP498 4.5 31.6 1.0 O A:HOH809 4.5 32.0 1.0 C3A A:CYC701 4.6 26.0 1.0 CHB A:CYC701 4.6 30.5 1.0 N A:GLN502 4.6 32.8 1.0 C4D A:CYC701 4.7 31.6 1.0 ND A:CYC701 4.8 31.3 1.0 O A:THR499 4.8 31.5 1.0 C A:LEU501 4.9 33.1 1.0 CD2 A:LEU501 5.0 32.9 1.0

X.-L.Xu, K.-H.Zhao, A.Hoeppner, W.Gaertner. Three-Dimensional Structure of the Parental and Photoproduct State of GAF3 From SLR1393 of Synechocystis Sp. PCC6803 To Be Published.