Magnesium in PDB 5c2c: GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form)

The structure of GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form), PDB code: 5c2c was solved by M.A.Arbing, V.A.Varaljay, S.Satagopan, F.R.Tabita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.36 / 2.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.220, 169.310, 76.690, 90.00, 119.20, 90.00
R / Rfree (%)	16.7 / 19.9

The structure of GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form) (pdb code 5c2c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form), PDB code: 5c2c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:42.5 occ:1.00 OD1 A:ASP193 2.1 51.5 1.0 OE1 A:GLU194 2.3 43.3 1.0 OQ2 A:KCX191 2.5 64.3 1.0 O A:HOH658 2.9 35.5 1.0 CD A:GLU194 3.3 41.5 1.0 CG A:ASP193 3.3 48.9 1.0 H A:GLU194 3.4 33.0 1.0 OE2 A:GLU194 3.5 45.7 1.0 HE2 A:HIS287 3.6 40.9 1.0 CX A:KCX191 3.6 60.3 1.0 HA A:ASP193 3.8 38.7 1.0 OQ1 A:KCX191 3.9 60.5 1.0 OD2 A:ASP193 3.9 53.3 1.0 HD2 A:LYS168 3.9 53.6 1.0 HG12 A:ILE164 4.2 52.7 1.0 NE2 A:HIS287 4.3 34.1 1.0 N A:GLU194 4.3 27.5 1.0 HG21 A:ILE164 4.3 54.1 1.0 HZ3 A:LYS168 4.4 54.7 1.0 CB A:ASP193 4.4 40.1 1.0 HB3 A:GLU194 4.5 33.4 1.0 CA A:ASP193 4.5 32.2 1.0 HD3 A:PRO195 4.6 39.4 1.0 CG A:GLU194 4.6 33.8 1.0 HE1 A:HIS287 4.7 40.2 1.0 HD13 A:ILE164 4.7 54.7 1.0 HB2 A:LYS168 4.7 51.0 1.0 NZ A:KCX191 4.7 55.2 1.0 HB2 A:ASP193 4.8 48.2 1.0 CE1 A:HIS287 4.8 33.5 1.0 CD A:LYS168 4.9 44.7 1.0 C A:ASP193 4.9 29.2 1.0 CB A:GLU194 5.0 27.8 1.0

Magnesium binding site 2 out of 6 in the GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:34.4 occ:1.00 OE1 A:GLN122 2.3 24.0 1.0 O A:HOH715 2.5 45.4 1.0 O A:SER299 2.5 30.1 1.0 O A:HOH740 2.6 32.9 1.0 O A:HOH637 2.7 24.3 1.0 O A:HOH706 2.9 29.5 1.0 HE22 A:GLN122 3.1 31.8 1.0 CD A:GLN122 3.2 25.8 1.0 HA A:LYS300 3.3 33.5 1.0 NE2 A:GLN122 3.5 26.5 1.0 HE22 A:GLN124 3.6 27.9 1.0 C A:SER299 3.7 29.0 1.0 HG22 A:THR304 4.2 31.6 1.0 CA A:LYS300 4.2 27.9 1.0 O A:HOH852 4.3 34.3 1.0 HG2 A:LYS300 4.3 39.5 1.0 O A:PRO297 4.3 36.5 1.0 HE21 A:GLN122 4.4 31.8 1.0 NE2 A:GLN124 4.4 23.3 1.0 N A:LYS300 4.4 28.8 1.0 HB3 A:GLN122 4.4 27.4 1.0 CG A:GLN122 4.6 23.4 1.0 O A:SER296 4.6 27.1 1.0 HA A:PRO297 4.7 39.5 1.0 HB3 A:SER299 4.8 34.0 1.0 HG A:SER299 4.8 32.0 1.0 CA A:SER299 4.8 28.2 1.0 OE1 A:GLN124 4.9 23.3 1.0 O A:HOH854 4.9 33.4 1.0 HB2 A:GLN122 4.9 27.4 1.0 CB A:GLN122 4.9 22.8 1.0 H A:SER299 4.9 35.1 1.0 HE21 A:GLN124 4.9 27.9 1.0 HG21 A:THR29 5.0 34.5 1.0 N A:SER299 5.0 29.3 1.0 CG2 A:THR304 5.0 26.3 1.0 HG2 A:GLN122 5.0 28.0 1.0

Magnesium binding site 3 out of 6 in the GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:51.7 occ:1.00 OD1 B:ASP193 2.2 48.3 1.0 OE1 B:GLU194 2.5 56.5 1.0 OQ2 B:KCX191 2.8 71.0 1.0 O B:HOH740 2.9 48.0 1.0 HD21 C:ASN111 3.0 63.9 1.0 CG B:ASP193 3.4 49.8 1.0 CD B:GLU194 3.5 54.2 1.0 HD22 C:ASN111 3.5 63.9 1.0 HE2 B:HIS287 3.5 47.9 1.0 ND2 C:ASN111 3.5 53.3 1.0 OE2 B:GLU194 3.6 56.2 1.0 H B:GLU194 3.7 44.0 1.0 CX B:KCX191 3.8 69.5 1.0 OD2 B:ASP193 3.9 56.9 1.0 OQ1 B:KCX191 4.0 73.9 1.0 HA B:ASP193 4.1 43.4 1.0 HD2 B:LYS168 4.1 76.2 1.0 NE2 B:HIS287 4.2 39.9 1.0 HG12 B:ILE164 4.3 54.8 1.0 HG21 B:ILE164 4.3 53.4 1.0 N B:GLU194 4.6 36.7 1.0 CB B:ASP193 4.6 42.8 1.0 HE1 B:HIS287 4.6 48.2 1.0 CG C:ASN111 4.6 49.8 1.0 HB3 B:GLU194 4.7 48.7 1.0 CA B:ASP193 4.7 36.1 1.0 HD13 B:ILE164 4.7 58.9 1.0 CE1 B:HIS287 4.8 40.1 1.0 HD3 B:PRO195 4.8 40.6 1.0 HB2 B:ASP193 4.8 51.4 1.0 CG B:GLU194 4.9 47.7 1.0 HB2 B:LYS168 5.0 75.2 1.0

Magnesium binding site 4 out of 6 in the GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:41.0 occ:1.00 OE1 B:GLN122 2.3 31.2 1.0 O B:HOH701 2.4 38.5 1.0 O B:HOH729 2.5 35.7 1.0 O B:SER299 2.6 38.4 1.0 O B:HOH637 2.7 36.6 1.0 HE22 B:GLN122 3.1 36.9 1.0 CD B:GLN122 3.2 30.1 1.0 HA B:LYS300 3.3 44.7 1.0 NE2 B:GLN122 3.5 30.8 1.0 HE22 B:GLN124 3.6 38.0 1.0 C B:SER299 3.7 38.9 1.0 HG22 B:THR304 4.2 44.6 1.0 CA B:LYS300 4.2 37.3 1.0 O B:PRO297 4.3 43.4 1.0 HG2 B:LYS300 4.3 54.1 1.0 O B:HOH794 4.3 39.9 1.0 HE21 B:GLN122 4.3 36.9 1.0 NE2 B:GLN124 4.4 31.7 1.0 N B:LYS300 4.4 38.3 1.0 HB3 B:GLN122 4.5 34.3 1.0 O B:HOH800 4.6 44.3 1.0 CG B:GLN122 4.6 28.0 1.0 O B:HOH786 4.6 47.8 1.0 O B:SER296 4.7 35.9 1.0 HA B:PRO297 4.7 47.2 1.0 HB3 B:SER299 4.9 44.7 1.0 HB2 B:GLN122 4.9 34.3 1.0 CA B:SER299 4.9 38.7 1.0 OE1 B:GLN124 4.9 34.1 1.0 CB B:GLN122 4.9 28.6 1.0 H B:SER299 5.0 47.8 1.0 HE21 B:GLN124 5.0 38.0 1.0 HG21 B:THR29 5.0 50.1 1.0 C B:PRO297 5.0 40.9 1.0 CG2 B:THR304 5.0 37.2 1.0 OG1 B:THR29 5.0 37.8 1.0

Magnesium binding site 5 out of 6 in the GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:52.4 occ:1.00 OD1 C:ASP193 2.1 56.0 1.0 OE1 C:GLU194 2.6 51.4 1.0 HD21 B:ASN111 3.0 65.7 1.0 OQ2 C:KCX191 3.1 73.4 1.0 CG C:ASP193 3.1 55.7 1.0 CD C:GLU194 3.4 48.3 1.0 OE2 C:GLU194 3.4 50.4 1.0 O C:HOH764 3.4 41.8 1.0 HD22 B:ASN111 3.4 65.7 1.0 ND2 B:ASN111 3.5 54.7 1.0 OD2 C:ASP193 3.5 62.6 1.0 HD2 C:LYS168 3.6 80.2 1.0 H C:GLU194 3.8 42.3 1.0 HE2 C:HIS287 4.0 51.1 1.0 HA C:ASP193 4.2 47.9 1.0 CX C:KCX191 4.3 70.6 1.0 HG21 C:ILE164 4.4 56.1 1.0 CB C:ASP193 4.4 47.3 1.0 CD C:LYS168 4.6 66.9 1.0 CG B:ASN111 4.6 51.5 1.0 HG12 C:ILE164 4.6 56.8 1.0 N C:GLU194 4.6 35.2 1.0 HD3 C:PRO195 4.6 40.7 1.0 HB2 C:LYS168 4.6 76.2 1.0 OQ1 C:KCX191 4.7 74.7 1.0 NE2 C:HIS287 4.7 42.6 1.0 HB2 C:ASP193 4.7 56.8 1.0 CA C:ASP193 4.8 39.9 1.0 HE2 C:LYS168 4.8 81.8 1.0 CG C:GLU194 4.8 41.3 1.0 HB3 C:GLU194 4.9 43.1 1.0 HD3 C:LYS168 4.9 80.2 1.0 HE1 C:HIS287 5.0 49.2 1.0

Magnesium binding site 6 out of 6 in the GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of GWS1B Rubisco: Form II Rubisco Derived From Uncultivated Gallionellacea Species (Unliganded Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:31.0 occ:1.00 O C:HOH720 2.3 28.4 1.0 OE1 C:GLN122 2.4 27.8 1.0 O C:HOH742 2.4 34.0 1.0 O C:HOH649 2.5 59.1 1.0 O C:HOH675 2.5 28.6 1.0 O C:SER299 2.6 34.0 1.0 HE22 C:GLN122 3.3 32.4 1.0 CD C:GLN122 3.3 29.4 1.0 HA C:LYS300 3.5 39.4 1.0 HE22 C:GLN124 3.6 32.2 1.0 NE2 C:GLN122 3.7 27.0 1.0 C C:SER299 3.8 34.5 1.0 HG22 C:THR304 4.1 35.7 1.0 HG1 C:THR29 4.2 33.1 1.0 O C:HOH798 4.2 37.8 1.0 CA C:LYS300 4.4 32.8 1.0 NE2 C:GLN124 4.4 26.8 1.0 O C:PRO297 4.4 39.0 1.0 HG2 C:LYS300 4.5 51.0 1.0 HB3 C:GLN122 4.5 33.8 1.0 HE21 C:GLN122 4.5 32.4 1.0 N C:LYS300 4.6 32.7 1.0 O C:SER296 4.7 30.0 1.0 CG C:GLN122 4.7 29.1 1.0 OE1 C:GLN124 4.7 29.6 1.0 HA C:PRO297 4.7 45.3 1.0 HG21 C:THR29 4.8 33.9 1.0 CG2 C:THR304 4.9 29.8 1.0 HE21 C:GLN124 4.9 32.2 1.0 HB3 C:SER299 4.9 42.2 1.0 HG21 C:THR304 4.9 35.7 1.0 O C:HOH768 4.9 52.6 1.0 OG1 C:THR29 4.9 27.6 1.0 CA C:SER299 5.0 36.2 1.0 CD C:GLN124 5.0 28.0 1.0

V.A.Varaljay, S.Satagopan, J.A.North, B.Witte, M.N.Dourado, K.Anantharaman, M.A.Arbing, S.H.Mccann, R.S.Oremland, J.F.Banfield, K.C.Wrighton, F.R.Tabita. Functional Metagenomic Selection of Ribulose 1, 5-Bisphosphate Carboxylase/Oxygenase From Uncultivated Bacteria. Environ.Microbiol. V. 18 1187 2016.
ISSN: ESSN 1462-2920
PubMed: 26617072
DOI: 10.1111/1462-2920.13138