Zinc in PDB 2i14: Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus

The structure of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus, PDB code: 2i14 was solved by D.H.Shin, R.Kim, S.-H.Kim, Berkeley Structural Genomics Center(Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.90
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	111.481, 111.481, 178.263, 90.00, 90.00, 120.00
R / Rfree (%)	24.7 / 28.2

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus (pdb code 2i14). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus, PDB code: 2i14:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn391 b:57.8 occ:1.00 SG A:CYS327 2.4 63.3 1.0 ND1 A:HIS331 2.6 73.4 1.0 SG A:CYS344 2.6 95.8 1.0 SG A:CYS347 2.7 0.2 1.0 CB A:CYS327 3.3 67.9 1.0 CG A:HIS331 3.3 71.8 1.0 O A:CYS347 3.4 99.8 1.0 CG1 A:VAL346 3.4 98.4 1.0 CB A:HIS331 3.5 69.1 1.0 CB A:CYS344 3.5 97.3 1.0 CE1 A:HIS331 3.6 73.8 1.0 CB A:ASN329 3.8 73.2 1.0 ND2 A:ASN329 3.9 73.9 1.0 CB A:CYS347 4.2 99.8 1.0 N A:CYS347 4.2 99.8 1.0 C A:CYS347 4.2 99.3 1.0 CB A:ALA349 4.4 92.7 1.0 CG A:ASN329 4.4 73.4 1.0 CA A:CYS347 4.4 99.8 1.0 CD2 A:HIS331 4.5 72.2 1.0 NE2 A:HIS331 4.6 72.8 1.0 N A:HIS331 4.7 68.5 1.0 N A:ASN329 4.7 74.0 1.0 CA A:HIS331 4.7 66.5 1.0 CA A:ASN329 4.7 73.6 1.0 CB A:VAL346 4.7 98.5 1.0 CA A:CYS327 4.8 68.9 1.0 C A:VAL346 4.8 99.7 1.0 CA A:CYS344 4.9 98.0 1.0 C A:ASN329 5.0 73.4 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn393 b:77.0 occ:1.00 OD2 A:ASP235 2.4 69.7 1.0 NE2 A:HIS178 2.5 66.7 1.0 OD1 A:ASP235 2.8 66.8 1.0 CG A:ASP235 2.8 67.8 1.0 CE1 A:HIS178 2.9 66.9 1.0 O A:ASP209 3.0 80.2 1.0 OD1 A:ASP209 3.1 85.3 1.0 CG A:ASP209 3.6 84.3 1.0 O A:ASP235 3.7 66.9 1.0 CD2 A:HIS178 3.7 66.3 1.0 CB A:ASP209 3.8 82.2 1.0 C A:ASP209 4.0 80.0 1.0 ND1 A:HIS178 4.2 66.7 1.0 C A:ASP235 4.2 67.0 1.0 NZ B:LYS714 4.2 73.3 1.0 CB A:ASP235 4.2 68.2 1.0 CD1 A:LEU207 4.4 69.2 1.0 OD2 A:ASP209 4.5 84.7 1.0 CA A:ASP209 4.5 80.0 1.0 CD A:PRO237 4.5 65.4 1.0 CG A:HIS178 4.6 66.5 1.0 CG A:PRO237 4.7 66.2 1.0 CA A:ASP235 4.7 67.5 1.0 CE B:LYS714 4.9 74.0 1.0 N A:ASP235 4.9 67.3 1.0 N A:THR236 4.9 66.6 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn791 b:78.1 occ:1.00 SG B:CYS727 2.3 69.7 1.0 ND1 B:HIS731 2.5 73.7 1.0 SG B:CYS744 2.6 97.0 1.0 SG B:CYS747 2.8 0.5 1.0 CG B:HIS731 3.3 72.8 1.0 CB B:CYS727 3.3 69.7 1.0 CG1 B:VAL746 3.4 98.9 1.0 O B:CYS747 3.4 99.9 1.0 CB B:HIS731 3.4 68.7 1.0 CE1 B:HIS731 3.6 74.4 1.0 CB B:CYS744 3.6 99.0 1.0 CB B:ASN729 3.8 75.2 1.0 ND2 B:ASN729 3.9 77.5 1.0 CB B:CYS747 4.2 0.9 1.0 N B:CYS747 4.2 0.1 1.0 C B:CYS747 4.3 99.6 1.0 CG B:ASN729 4.4 76.2 1.0 CB B:ALA749 4.4 93.2 1.0 CD2 B:HIS731 4.4 74.1 1.0 CA B:CYS747 4.5 0.1 1.0 NE2 B:HIS731 4.5 74.5 1.0 N B:HIS731 4.6 68.1 1.0 CA B:HIS731 4.6 65.6 1.0 N B:ASN729 4.6 74.6 1.0 CA B:ASN729 4.7 74.7 1.0 CA B:CYS727 4.7 70.3 1.0 CB B:VAL746 4.7 99.7 1.0 C B:VAL746 4.9 0.1 1.0 C B:ASN729 4.9 74.8 1.0 CA B:CYS744 5.0 99.4 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn793 b:85.5 occ:1.00 OD2 B:ASP635 2.3 70.4 1.0 NE2 B:HIS578 2.5 67.5 1.0 OD1 B:ASP635 2.7 70.4 1.0 CG B:ASP635 2.8 69.6 1.0 CE1 B:HIS578 2.9 66.5 1.0 O B:ASP609 3.0 81.8 1.0 OD1 B:ASP609 3.1 86.6 1.0 CG B:ASP609 3.6 84.5 1.0 O B:ASP635 3.7 66.4 1.0 CD2 B:HIS578 3.7 66.9 1.0 CB B:ASP609 3.8 82.7 1.0 C B:ASP609 4.0 80.9 1.0 CB B:ASP635 4.2 68.1 1.0 ND1 B:HIS578 4.2 66.0 1.0 C B:ASP635 4.2 66.8 1.0 CD1 B:LEU607 4.3 67.3 1.0 NZ A:LYS314 4.4 74.8 1.0 CA B:ASP609 4.5 80.8 1.0 OD2 B:ASP609 4.5 85.2 1.0 CG B:HIS578 4.6 66.4 1.0 CD B:PRO637 4.6 66.7 1.0 CA B:ASP635 4.7 67.1 1.0 CG B:PRO637 4.8 65.8 1.0 N B:ASP635 4.8 67.2 1.0 N B:THR636 4.9 66.4 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1391 b:62.3 occ:1.00 SG C:CYS1327 2.3 64.6 1.0 SG C:CYS1344 2.6 93.5 1.0 ND1 C:HIS1331 2.6 72.0 1.0 SG C:CYS1347 2.7 0.5 1.0 CB C:CYS1327 3.3 67.8 1.0 O C:CYS1347 3.3 99.7 1.0 CG C:HIS1331 3.3 70.6 1.0 CG1 C:VAL1346 3.4 97.9 1.0 CB C:HIS1331 3.5 68.4 1.0 CB C:CYS1344 3.5 97.1 1.0 CE1 C:HIS1331 3.6 72.9 1.0 CB C:ASN1329 3.9 73.3 1.0 ND2 C:ASN1329 3.9 74.8 1.0 CB C:CYS1347 4.2 0.7 1.0 C C:CYS1347 4.2 99.5 1.0 N C:CYS1347 4.2 100.0 1.0 CB C:ALA1349 4.4 92.5 1.0 CG C:ASN1329 4.4 73.7 1.0 CA C:CYS1347 4.5 0.1 1.0 CD2 C:HIS1331 4.5 71.8 1.0 NE2 C:HIS1331 4.6 72.5 1.0 N C:HIS1331 4.7 67.2 1.0 CA C:HIS1331 4.7 65.2 1.0 N C:ASN1329 4.7 73.6 1.0 CA C:ASN1329 4.7 73.0 1.0 CA C:CYS1327 4.7 68.1 1.0 CB C:VAL1346 4.7 98.1 1.0 C C:VAL1346 4.8 99.8 1.0 CA C:CYS1344 4.9 97.7 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1393 b:85.3 occ:1.00 OD2 C:ASP1235 2.4 71.8 1.0 NE2 C:HIS1178 2.4 67.4 1.0 OD1 C:ASP1235 2.8 68.2 1.0 CG C:ASP1235 2.9 69.3 1.0 CE1 C:HIS1178 2.9 67.4 1.0 O C:ASP1209 3.0 80.3 1.0 OD1 C:ASP1209 3.1 86.5 1.0 CG C:ASP1209 3.6 84.9 1.0 O C:ASP1235 3.7 64.9 1.0 CD2 C:HIS1178 3.7 66.9 1.0 CB C:ASP1209 3.8 82.4 1.0 C C:ASP1209 4.0 80.0 1.0 ND1 C:HIS1178 4.1 67.1 1.0 NZ D:LYS1714 4.2 74.1 1.0 C C:ASP1235 4.2 65.4 1.0 CB C:ASP1235 4.2 67.7 1.0 CD1 C:LEU1207 4.4 69.0 1.0 CA C:ASP1209 4.5 80.2 1.0 OD2 C:ASP1209 4.5 85.0 1.0 CD C:PRO1237 4.6 65.8 1.0 CG C:HIS1178 4.6 66.7 1.0 CA C:ASP1235 4.7 66.5 1.0 CG C:PRO1237 4.7 65.8 1.0 CE D:LYS1714 4.9 74.3 1.0 N C:ASP1235 4.9 66.5 1.0 N C:THR1236 4.9 64.5 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1791 b:77.5 occ:1.00 SG D:CYS1727 2.4 68.0 1.0 ND1 D:HIS1731 2.5 74.3 1.0 SG D:CYS1744 2.6 98.9 1.0 SG D:CYS1747 2.8 0.3 1.0 CG D:HIS1731 3.3 73.4 1.0 CB D:CYS1727 3.3 68.5 1.0 CG1 D:VAL1746 3.3 99.1 1.0 CB D:HIS1731 3.4 69.7 1.0 O D:CYS1747 3.4 0.7 1.0 CB D:CYS1744 3.5 99.5 1.0 CE1 D:HIS1731 3.5 75.0 1.0 CB D:ASN1729 3.9 75.0 1.0 ND2 D:ASN1729 3.9 76.2 1.0 N D:CYS1747 4.2 0.4 1.0 CB D:CYS1747 4.3 0.0 1.0 C D:CYS1747 4.3 0.2 1.0 CG D:ASN1729 4.4 75.6 1.0 CB D:ALA1749 4.4 92.8 1.0 CD2 D:HIS1731 4.4 74.5 1.0 CA D:CYS1747 4.5 0.5 1.0 NE2 D:HIS1731 4.5 75.8 1.0 CA D:HIS1731 4.6 66.7 1.0 N D:HIS1731 4.6 69.2 1.0 N D:ASN1729 4.7 74.3 1.0 CA D:ASN1729 4.7 74.6 1.0 CB D:VAL1746 4.7 99.6 1.0 CA D:CYS1727 4.7 69.7 1.0 C D:VAL1746 4.8 0.4 1.0 C D:ASN1729 4.9 74.7 1.0 CA D:CYS1744 5.0 99.9 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1793 b:84.2 occ:1.00 OD2 D:ASP1635 2.3 70.6 1.0 NE2 D:HIS1578 2.4 65.9 1.0 OD1 D:ASP1635 2.7 68.3 1.0 CG D:ASP1635 2.8 68.8 1.0 CE1 D:HIS1578 2.9 65.8 1.0 O D:ASP1609 3.0 81.8 1.0 OD1 D:ASP1609 3.1 86.9 1.0 CG D:ASP1609 3.6 85.0 1.0 CD2 D:HIS1578 3.7 65.8 1.0 O D:ASP1635 3.7 68.7 1.0 CB D:ASP1609 3.8 82.7 1.0 C D:ASP1609 4.0 80.9 1.0 ND1 D:HIS1578 4.1 65.4 1.0 CB D:ASP1635 4.2 68.7 1.0 C D:ASP1635 4.2 68.2 1.0 CD1 D:LEU1607 4.3 69.2 1.0 NZ C:LYS1314 4.3 74.9 1.0 CA D:ASP1609 4.5 80.4 1.0 OD2 D:ASP1609 4.5 85.5 1.0 CG D:HIS1578 4.6 65.9 1.0 CD D:PRO1637 4.6 66.6 1.0 CA D:ASP1635 4.7 68.6 1.0 CG D:PRO1637 4.8 66.3 1.0 N D:ASP1635 4.8 68.3 1.0 N D:THR1636 4.9 67.9 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2391 b:82.1 occ:1.00 SG E:CYS2344 2.5 94.7 1.0 SG E:CYS2327 2.5 70.6 1.0 ND1 E:HIS2331 2.6 74.2 1.0 SG E:CYS2347 2.8 0.6 1.0 CB E:CYS2327 3.3 69.4 1.0 O E:CYS2347 3.3 98.6 1.0 CG1 E:VAL2346 3.3 99.4 1.0 CG E:HIS2331 3.4 73.8 1.0 CB E:CYS2344 3.4 97.5 1.0 CB E:HIS2331 3.5 69.7 1.0 CE1 E:HIS2331 3.7 75.3 1.0 CB E:ASN2329 4.0 74.0 1.0 ND2 E:ASN2329 4.0 73.7 1.0 C E:CYS2347 4.2 98.9 1.0 N E:CYS2347 4.2 99.6 1.0 CB E:CYS2347 4.3 0.3 1.0 CB E:ALA2349 4.4 93.0 1.0 CA E:CYS2347 4.4 99.7 1.0 CG E:ASN2329 4.5 74.4 1.0 CD2 E:HIS2331 4.6 75.0 1.0 NE2 E:HIS2331 4.7 75.9 1.0 CA E:HIS2331 4.7 66.2 1.0 CB E:VAL2346 4.7 99.4 1.0 N E:HIS2331 4.7 67.8 1.0 CA E:CYS2327 4.7 70.5 1.0 N E:ASN2329 4.7 73.0 1.0 C E:VAL2346 4.8 99.2 1.0 CA E:ASN2329 4.8 73.3 1.0 CA E:CYS2344 4.8 98.2 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2393 b:77.4 occ:1.00 OD2 E:ASP2235 2.2 71.0 1.0 NE2 E:HIS2178 2.5 65.5 1.0 OD1 E:ASP2235 2.6 66.9 1.0 CG E:ASP2235 2.7 69.9 1.0 CE1 E:HIS2178 2.9 66.3 1.0 O E:ASP2209 3.0 79.7 1.0 OD1 E:ASP2209 3.1 84.1 1.0 O E:ASP2235 3.6 68.4 1.0 CG E:ASP2209 3.6 84.3 1.0 CD2 E:HIS2178 3.7 65.5 1.0 CB E:ASP2209 3.8 82.0 1.0 C E:ASP2209 4.0 79.6 1.0 CB E:ASP2235 4.1 69.9 1.0 C E:ASP2235 4.1 68.5 1.0 ND1 E:HIS2178 4.2 66.7 1.0 CD1 E:LEU2207 4.4 67.9 1.0 NZ F:LYS2714 4.5 71.9 1.0 CA E:ASP2209 4.5 79.5 1.0 OD2 E:ASP2209 4.5 86.0 1.0 CA E:ASP2235 4.6 69.2 1.0 CG E:HIS2178 4.6 65.7 1.0 CD E:PRO2237 4.6 64.6 1.0 N E:ASP2235 4.8 69.4 1.0 CG E:PRO2237 4.8 64.4 1.0 N E:THR2236 4.9 67.8 1.0

D.H.Shin, R.Kim, S.-H.Kim, R.Pufan, H.Yokota. Crystal Structure of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus To Be Published.