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Magnesium in PDB 2vpn: High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata

Protein crystallography data

The structure of High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata, PDB code: 2vpn was solved by S.I.Kuhlmann, A.C.Terwisscha Van Scheltinga, R.Bienert, H.J.Kunte, C.Ziegler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.300, 52.200, 63.500, 80.80, 85.80, 77.90
R / Rfree (%) 15.8 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata (pdb code 2vpn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata, PDB code: 2vpn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2vpn

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Magnesium binding site 1 out of 8 in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1312

b:25.5
occ:1.00
 O A:HOH2152 2.0 27.4 1.0
O A:HOH2150 2.1 32.0 1.0
ND2 A:ASN140 2.1 16.3 0.8
CG A:ASN140 3.4 19.4 0.8
O A:HOH2154 3.7 32.9 1.0
OD1 A:ASN140 3.9 25.0 0.8
O A:HOH2165 4.1 20.6 1.0
CB A:ASN140 4.3 17.4 0.2
O A:HOH2061 4.3 22.2 1.0
O A:HOH2151 4.3 16.2 1.0
OD1 A:ASP139 4.4 23.8 1.0
O A:HOH2060 4.5 37.0 1.0
CB A:ASN140 4.6 19.2 0.8
CA A:ASN140 4.7 16.6 0.2
CA A:ASN140 4.7 17.1 0.8
N A:ASN140 4.8 17.5 1.0

Magnesium binding site 2 out of 8 in 2vpn

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Magnesium binding site 2 out of 8 in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1313

b:14.3
occ:1.00
 O A:HOH2265 2.1 14.0 1.0
O A:HOH2106 2.1 14.3 1.0
O A:HOH2108 2.1 14.2 1.0
O A:HOH2264 2.1 12.8 1.0
O A:HOH2262 2.1 13.9 1.0
O B:HOH2090 2.2 14.7 1.0
O A:ALA259 4.1 15.8 1.0
O A:ALA260 4.2 14.4 1.0
O B:ILE56 4.2 11.1 1.0
O A:HOH2270 4.2 23.4 1.0
O B:HOH2093 4.2 10.0 1.0
O A:HOH2268 4.2 17.3 1.0
O A:HOH2107 4.4 23.5 1.0
O B:HOH2092 4.5 37.9 1.0
O A:HOH2269 4.5 13.9 1.0
NH1 B:ARG4 4.6 14.5 1.0
O B:GLY55 4.7 15.2 1.0
C A:ALA260 4.7 14.2 1.0
CA B:ILE56 4.8 12.7 1.0
NE2 B:GLN58 4.9 11.3 1.0
C B:ILE56 5.0 11.3 1.0
CA A:ALA260 5.0 13.6 1.0

Magnesium binding site 3 out of 8 in 2vpn

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Magnesium binding site 3 out of 8 in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1314

b:34.6
occ:1.00
 O A:HOH2258 2.0 23.8 1.0
O B:HOH2062 2.1 24.6 1.0
O A:HOH2254 2.2 22.2 1.0
OE1 B:GLN35 4.0 21.1 1.0
O B:HOH2063 4.0 41.8 1.0
OE1 A:GLU255 4.1 23.6 1.0
O B:HOH2007 4.1 18.2 1.0
O A:HOH2256 4.2 41.7 1.0
OE2 A:GLU255 4.2 27.4 1.0
CD A:GLU255 4.6 22.3 1.0
O A:HOH2257 4.7 11.7 1.0

Magnesium binding site 4 out of 8 in 2vpn

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Magnesium binding site 4 out of 8 in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1315

b:26.2
occ:1.00
 O A:HOH2141 1.9 24.3 1.0
O A:HOH2143 2.1 33.7 1.0
O A:HOH2145 2.1 27.1 1.0
O A:HOH2147 2.2 27.9 1.0
O A:HOH2148 4.1 39.2 1.0
O A:GLU136 4.2 17.6 1.0
O A:ASP137 4.2 14.3 1.0
NZ A:LYS141 4.3 20.7 0.5
O A:ASP139 4.4 15.2 1.0
OE2 A:GLU130 4.4 28.4 1.0
CA A:ASP137 4.5 13.7 1.0
OE1 A:GLU130 4.5 31.2 1.0
C A:ASP137 4.7 13.3 1.0
OD1 A:ASP137 4.8 20.9 1.0
CD A:GLU130 4.8 24.5 1.0

Magnesium binding site 5 out of 8 in 2vpn

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Magnesium binding site 5 out of 8 in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1312

b:32.6
occ:1.00
 O B:HOH2059 2.0 19.8 1.0
O B:HOH2043 2.3 36.8 1.0
O B:GLU27 2.4 18.7 1.0
O B:SER30 2.4 18.9 1.0
O B:HOH2040 2.4 32.3 1.0
O B:HOH2054 2.7 45.0 1.0
C B:GLU27 3.4 18.1 1.0
C B:SER30 3.5 18.0 1.0
O B:HOH2019 3.9 37.5 1.0
CA B:GLU27 4.0 16.9 1.0
CA B:ASP31 4.0 19.1 1.0
N B:ASP31 4.2 18.5 1.0
O B:HOH2045 4.4 38.2 1.0
OD1 B:ASP31 4.5 26.9 0.5
O B:HOH2056 4.5 41.4 1.0
O B:HIS32 4.5 16.9 1.0
CB B:GLU27 4.5 16.2 1.0
C B:ASP31 4.6 18.7 1.0
N B:ASP28 4.6 17.4 1.0
N B:SER30 4.6 19.4 1.0
CA B:SER30 4.7 19.1 1.0
CA B:ASP28 4.9 19.3 1.0

Magnesium binding site 6 out of 8 in 2vpn

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Magnesium binding site 6 out of 8 in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1313

b:30.8
occ:1.00
 O B:HOH2123 1.9 32.4 1.0
O B:HOH2127 2.0 41.4 1.0
O B:HOH2274 2.0 17.5 1.0
O B:HOH2272 2.0 20.8 1.0
O B:HOH2291 2.1 33.0 1.0
O B:HOH2280 2.5 41.3 1.0
O B:LYS247 3.9 13.5 1.0
O B:HIS245 4.0 10.8 1.0
O B:HOH2294 4.2 21.3 1.0
O B:HOH2275 4.3 29.5 1.0
OE1 B:GLU252 4.6 25.6 1.0
O B:GLU244 4.8 12.8 1.0
O B:HOH2270 4.8 42.6 1.0
C B:HIS245 4.9 9.7 1.0

Magnesium binding site 7 out of 8 in 2vpn

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Magnesium binding site 7 out of 8 in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1314

b:35.8
occ:1.00
 O B:HOH2074 2.0 34.4 1.0
O B:HOH2185 2.2 29.1 1.0
O B:HOH2180 2.2 25.6 1.0
O B:HOH2087 3.7 36.2 1.0
OD2 B:ASP137 4.1 17.9 1.0
O B:PRO131 4.2 17.6 1.0
O B:HOH2137 4.2 35.9 1.0
OD1 B:ASP137 4.3 20.8 1.0
OE1 B:GLU130 4.4 31.1 1.0
CG B:ASP137 4.5 17.1 1.0
OG1 B:THR133 4.8 25.5 1.0

Magnesium binding site 8 out of 8 in 2vpn

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Magnesium binding site 8 out of 8 in the High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of High-Resolution Structure of the Periplasmic Ectoine- Binding Protein From Teaabc Trap-Transporter of Halomonas Elongata within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1315

b:35.9
occ:1.00
 O B:HOH2085 2.0 35.4 1.0
O B:HOH2179 2.0 28.3 1.0
O B:HOH2183 2.3 26.3 1.0
O B:HOH2186 2.3 23.0 1.0
OE2 B:GLU130 4.0 29.5 1.0
OE1 B:GLU130 4.2 31.1 1.0
O B:ASP137 4.3 14.6 1.0
CD B:GLU130 4.5 24.6 1.0
O B:GLU136 4.5 17.4 1.0
CA B:ASP137 4.6 13.5 1.0
OD1 B:ASP137 4.7 20.8 1.0
C B:ASP137 4.8 13.2 1.0
O B:ASP139 4.9 15.9 1.0
CE B:LYS141 5.0 21.6 1.0

Reference:

S.I.Kuhlmann, A.C.Terwisscha Van Scheltinga, R.Bienert, H.J.Kunte, C.Ziegler. 1.55 A Structure of the Ectoine Binding Protein Teaa of the Osmoregulated Trap-Transporter Teaabc From Halomonas Elongata. Biochemistry V. 47 9475 2008.
ISSN: ISSN 0006-2960
PubMed: 18702523
DOI: 10.1021/BI8006719
Page generated: Wed Aug 14 05:17:52 2024

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