Iron in PDB 4v0h: Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1)

The structure of Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1), PDB code: 4v0h was solved by I.Pettinati, M.A.Mcdonough, J.Brem, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.96 / 1.79
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.950, 67.130, 67.900, 109.31, 105.40, 90.17
R / Rfree (%)	18.2 / 21.1

The binding sites of Iron atom in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1) (pdb code 4v0h). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1), PDB code: 4v0h:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1242 b:25.8 occ:1.00 OD2 A:ASP195 2.1 24.0 1.0 O A:HOH2077 2.2 26.8 1.0 NE2 A:HIS172 2.3 24.5 1.0 NE2 A:HIS117 2.3 17.5 1.0 ND1 A:HIS119 2.3 22.5 1.0 O A:HOH2078 2.4 29.3 1.0 FE A:FE1243 3.0 24.3 0.5 CD2 A:HIS172 3.2 25.8 1.0 CG A:ASP195 3.2 25.4 1.0 CD2 A:HIS117 3.2 17.7 1.0 CE1 A:HIS119 3.2 28.0 1.0 CE1 A:HIS172 3.3 28.1 1.0 CE1 A:HIS117 3.4 20.4 1.0 CG A:HIS119 3.4 18.7 1.0 CB A:ASP195 3.7 21.6 1.0 CB A:HIS119 3.7 20.2 1.0 NE2 A:HIS122 4.0 22.4 1.0 CD2 A:HIS122 4.1 21.2 1.0 OD1 A:ASP195 4.2 30.0 1.0 CG A:HIS172 4.3 24.8 1.0 ND1 A:HIS172 4.3 24.2 1.0 NE2 A:HIS119 4.4 27.5 1.0 CG A:HIS117 4.4 16.0 1.0 ND1 A:HIS117 4.4 15.7 1.0 CD2 A:HIS119 4.5 28.4 1.0 OD1 A:ASP121 4.6 27.8 1.0 NE2 A:HIS234 4.8 23.9 1.0

Iron binding site 2 out of 8 in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1243 b:24.3 occ:0.50 O A:HOH2077 2.1 26.8 1.0 NE2 A:HIS234 2.1 23.9 1.0 OD2 A:ASP195 2.1 24.0 1.0 NE2 A:HIS122 2.4 22.4 1.0 OD2 A:ASP121 2.9 34.5 1.0 CE1 A:HIS234 3.0 22.5 1.0 CG A:ASP195 3.0 25.4 1.0 FE A:FE1242 3.0 25.8 1.0 CD2 A:HIS122 3.0 21.2 1.0 CD2 A:HIS234 3.1 23.8 1.0 OD1 A:ASP195 3.1 30.0 1.0 OD1 A:ASP121 3.4 27.8 1.0 CG A:ASP121 3.5 26.3 1.0 CE1 A:HIS122 3.6 26.5 1.0 O A:HOH2078 3.7 29.3 1.0 ND1 A:HIS234 4.1 24.3 1.0 NE2 A:HIS117 4.2 17.5 1.0 CG A:HIS234 4.2 22.2 1.0 CG A:HIS122 4.3 18.1 1.0 CB A:ASP195 4.4 21.6 1.0 CE1 A:HIS117 4.4 20.4 1.0 ND1 A:HIS122 4.5 26.3 1.0 NE2 A:HIS172 4.8 24.5 1.0 CB A:ASP121 4.9 20.2 1.0 ND1 A:HIS119 4.9 22.5 1.0 CB A:HIS119 5.0 20.2 1.0

Iron binding site 3 out of 8 in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1242 b:23.4 occ:1.00 O B:HOH2083 2.1 24.4 1.0 OD2 B:ASP195 2.2 19.1 1.0 ND1 B:HIS119 2.3 24.3 1.0 NE2 B:HIS117 2.4 15.9 1.0 NE2 B:HIS172 2.4 23.1 1.0 O B:HOH2086 2.5 30.5 1.0 FE B:FE1243 3.0 23.0 0.5 CD2 B:HIS172 3.1 19.3 1.0 CE1 B:HIS119 3.2 25.7 1.0 CD2 B:HIS117 3.2 16.6 1.0 CG B:ASP195 3.3 22.2 1.0 CG B:HIS119 3.3 16.9 1.0 CE1 B:HIS117 3.4 19.6 1.0 CE1 B:HIS172 3.4 23.9 1.0 CB B:HIS119 3.7 16.1 1.0 CB B:ASP195 3.8 16.6 1.0 NE2 B:HIS122 4.0 17.6 1.0 CD2 B:HIS122 4.0 21.7 1.0 C1 B:GOL1244 4.2 49.9 0.5 OD1 B:ASP195 4.3 28.4 1.0 NE2 B:HIS119 4.3 28.2 1.0 CG B:HIS172 4.3 19.2 1.0 C1 B:GOL1244 4.4 50.4 0.5 CG B:HIS117 4.4 15.3 1.0 CD2 B:HIS119 4.4 32.6 1.0 ND1 B:HIS172 4.4 22.6 1.0 ND1 B:HIS117 4.5 14.9 1.0 C3 B:GOL1244 4.5 51.5 0.5 O3 B:GOL1244 4.6 49.9 0.5 O1 B:GOL1244 4.6 49.4 0.5 OD1 B:ASP121 4.7 29.5 1.0 NE2 B:HIS234 4.7 23.0 1.0 C3 B:GOL1244 4.7 51.4 0.5 C2 B:GOL1244 4.7 51.0 0.5 C2 B:GOL1244 4.9 51.1 0.5

Iron binding site 4 out of 8 in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1243 b:23.0 occ:0.50 O B:HOH2083 2.0 24.4 1.0 NE2 B:HIS234 2.0 23.0 1.0 OD2 B:ASP195 2.1 19.1 1.0 NE2 B:HIS122 2.3 17.6 1.0 CE1 B:HIS234 2.9 18.6 1.0 CD2 B:HIS122 2.9 21.7 1.0 FE B:FE1242 3.0 23.4 1.0 CG B:ASP195 3.0 22.2 1.0 OD2 B:ASP121 3.0 41.5 1.0 CD2 B:HIS234 3.1 19.8 1.0 OD1 B:ASP195 3.1 28.4 1.0 O3 B:GOL1244 3.3 49.9 0.5 CE1 B:HIS122 3.4 22.4 1.0 OD1 B:ASP121 3.5 29.5 1.0 CG B:ASP121 3.6 27.2 1.0 C3 B:GOL1244 3.6 51.5 0.5 O B:HOH2086 3.8 30.5 1.0 C3 B:GOL1244 3.9 51.4 0.5 ND1 B:HIS234 4.0 19.7 1.0 NE2 B:HIS117 4.2 15.9 1.0 CG B:HIS234 4.2 17.0 1.0 CG B:HIS122 4.2 16.7 1.0 O3 B:GOL1244 4.3 53.0 0.5 CB B:ASP195 4.4 16.6 1.0 ND1 B:HIS122 4.4 21.9 1.0 CE1 B:HIS117 4.4 19.6 1.0 O1 B:GOL1244 4.7 49.4 0.5 C1 B:GOL1244 4.7 49.9 0.5 C2 B:GOL1244 4.7 51.0 0.5 ND1 B:HIS119 4.8 24.3 1.0 C1 B:GOL1244 4.8 50.4 0.5 NE2 B:HIS172 4.8 23.1 1.0 CB B:ASP121 4.9 21.6 1.0 C2 B:GOL1244 4.9 51.1 0.5 O1 B:GOL1244 4.9 51.2 0.5 CB B:HIS119 5.0 16.1 1.0 OE2 B:GLU198 5.0 61.4 1.0

Iron binding site 5 out of 8 in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1242 b:22.6 occ:1.00 O C:HOH2066 2.1 29.0 1.0 OD2 C:ASP195 2.1 17.0 1.0 NE2 C:HIS172 2.3 20.9 1.0 ND1 C:HIS119 2.3 20.9 1.0 NE2 C:HIS117 2.3 14.4 1.0 O C:HOH2067 2.4 28.4 1.0 FE C:FE1243 3.0 22.8 0.5 CD2 C:HIS172 3.1 21.8 1.0 CE1 C:HIS119 3.1 25.9 1.0 CG C:ASP195 3.2 22.7 1.0 CD2 C:HIS117 3.2 15.2 1.0 CE1 C:HIS172 3.3 24.0 1.0 CE1 C:HIS117 3.3 21.9 1.0 CG C:HIS119 3.4 19.8 1.0 CB C:HIS119 3.7 17.6 1.0 CB C:ASP195 3.7 18.0 1.0 NE2 C:HIS122 4.0 20.4 1.0 CD2 C:HIS122 4.1 18.3 1.0 OD1 C:ASP195 4.3 27.3 1.0 CG C:HIS172 4.3 19.7 1.0 NE2 C:HIS119 4.3 26.0 1.0 ND1 C:HIS172 4.3 22.0 1.0 ND1 C:HIS117 4.4 14.5 1.0 CG C:HIS117 4.4 14.4 1.0 CD2 C:HIS119 4.4 26.3 1.0 O2 C:GOL1244 4.5 56.6 1.0 C3 C:GOL1244 4.6 55.1 1.0 O3 C:GOL1244 4.7 60.0 1.0 OD1 C:ASP121 4.7 25.0 1.0 NE2 C:HIS234 4.8 24.8 1.0 C2 C:GOL1244 4.9 52.4 1.0

Iron binding site 6 out of 8 in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1243 b:22.8 occ:0.50 O C:HOH2066 2.0 29.0 1.0 OD2 C:ASP195 2.0 17.0 1.0 NE2 C:HIS234 2.1 24.8 1.0 NE2 C:HIS122 2.3 20.4 1.0 CG C:ASP195 2.9 22.7 1.0 FE C:FE1242 3.0 22.6 1.0 CD2 C:HIS122 3.0 18.3 1.0 CD2 C:HIS234 3.0 25.6 1.0 OD2 C:ASP121 3.0 36.9 1.0 CE1 C:HIS234 3.1 21.1 1.0 OD1 C:ASP195 3.1 27.3 1.0 CE1 C:HIS122 3.4 24.4 1.0 OD1 C:ASP121 3.6 25.0 1.0 O2 C:GOL1244 3.6 56.6 1.0 O C:HOH2067 3.6 28.4 1.0 CG C:ASP121 3.6 24.9 1.0 CG C:HIS234 4.2 22.1 1.0 ND1 C:HIS234 4.2 21.9 1.0 NE2 C:HIS117 4.2 14.4 1.0 CG C:HIS122 4.3 17.0 1.0 CB C:ASP195 4.4 18.0 1.0 CE1 C:HIS117 4.4 21.9 1.0 ND1 C:HIS122 4.4 25.8 1.0 O3 C:GOL1244 4.6 60.0 1.0 NE2 C:HIS172 4.7 20.9 1.0 C2 C:GOL1244 4.7 52.4 1.0 ND1 C:HIS119 4.8 20.9 1.0 C3 C:GOL1244 5.0 55.1 1.0 CB C:ASP121 5.0 17.1 1.0 CB C:HIS119 5.0 17.6 1.0

Iron binding site 7 out of 8 in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1243 b:24.6 occ:1.00 OD2 D:ASP195 2.2 21.1 1.0 O D:HOH2066 2.2 27.1 1.0 ND1 D:HIS119 2.3 23.9 1.0 NE2 D:HIS117 2.3 15.8 1.0 NE2 D:HIS172 2.4 20.7 1.0 O D:HOH2068 2.4 31.7 1.0 FE D:FE1244 2.9 24.8 0.5 CE1 D:HIS119 3.1 26.3 1.0 CD2 D:HIS172 3.2 25.6 1.0 CD2 D:HIS117 3.2 20.1 1.0 CG D:ASP195 3.2 23.9 1.0 CE1 D:HIS117 3.4 22.8 1.0 CG D:HIS119 3.4 22.0 1.0 CE1 D:HIS172 3.4 26.3 1.0 CB D:ASP195 3.7 17.1 1.0 CB D:HIS119 3.8 18.4 1.0 NE2 D:HIS122 4.1 22.4 1.0 O2 D:GOL1245 4.1 49.8 0.5 CD2 D:HIS122 4.1 22.4 1.0 OD1 D:ASP195 4.3 29.0 1.0 NE2 D:HIS119 4.3 27.6 1.0 CG D:HIS172 4.4 22.5 1.0 CG D:HIS117 4.4 15.2 1.0 ND1 D:HIS117 4.4 15.2 1.0 CD2 D:HIS119 4.4 27.7 1.0 ND1 D:HIS172 4.5 25.3 1.0 O1 D:GOL1245 4.5 39.8 0.5 O2 D:GOL1245 4.6 49.6 0.5 C2 D:GOL1245 4.6 48.4 0.5 C1 D:GOL1245 4.6 45.0 0.5 OD1 D:ASP121 4.7 26.1 1.0 C1 D:GOL1245 4.7 45.2 0.5 NE2 D:HIS234 4.7 27.7 1.0 C2 D:GOL1245 4.8 48.1 0.5

Iron binding site 8 out of 8 in the Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Human Metallo Beta Lactamase Domain Containing Protein 1 (HMBLAC1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1244 b:24.8 occ:0.50 O D:HOH2066 2.0 27.1 1.0 NE2 D:HIS234 2.1 27.7 1.0 OD2 D:ASP195 2.1 21.1 1.0 NE2 D:HIS122 2.4 22.4 1.0 OD2 D:ASP121 2.7 37.9 1.0 FE D:FE1243 2.9 24.6 1.0 CE1 D:HIS234 3.0 24.1 1.0 CD2 D:HIS122 3.0 22.4 1.0 CG D:ASP195 3.0 23.9 1.0 CD2 D:HIS234 3.1 26.0 1.0 OD1 D:ASP195 3.2 29.0 1.0 O1 D:GOL1245 3.4 39.8 0.5 CG D:ASP121 3.4 26.5 1.0 OD1 D:ASP121 3.5 26.1 1.0 O D:HOH2068 3.6 31.7 1.0 CE1 D:HIS122 3.6 27.3 1.0 C1 D:GOL1245 3.7 45.2 0.5 C1 D:GOL1245 3.8 45.0 0.5 NE2 D:HIS117 4.1 15.8 1.0 ND1 D:HIS234 4.1 24.1 1.0 CG D:HIS234 4.2 20.2 1.0 CG D:HIS122 4.3 18.6 1.0 O1 D:GOL1245 4.3 44.2 0.5 O2 D:GOL1245 4.4 49.8 0.5 CB D:ASP195 4.4 17.1 1.0 CE1 D:HIS117 4.4 22.8 1.0 ND1 D:HIS122 4.5 27.1 1.0 C2 D:GOL1245 4.6 48.4 0.5 C2 D:GOL1245 4.6 48.1 0.5 ND1 D:HIS119 4.7 23.9 1.0 O2 D:GOL1245 4.8 49.6 0.5 NE2 D:HIS172 4.8 20.7 1.0 CB D:ASP121 4.8 20.1 1.0 CB D:HIS119 4.9 18.4 1.0

I.Pettinati, P.Grzechnik, C.Ribeiro De Almeida, J.Brem, M.A.Mcdonough, S.Dhir, N.J.Proudfoot, C.J.Schofield. Biosynthesis of Histone Messenger Rna Employs A Specific 3' End Endonuclease. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30507380
DOI: 10.7554/ELIFE.39865